From owner-software@net.bio.net Sat Mar 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!Germany.EU.net!Dortmund.Germany.EU.net!gsf.de!news From: Burkhard Morgenstern Newsgroups: bionet.software Subject: DIALIGN alignment program for LINUX Date: Thu, 27 Feb 1997 13:39:22 +0100 Organization: GSF Forschungszentrum fuer Umwelt und Gesundheit mbH Lines: 56 Message-ID: <3315807A.41C6@gsf.de> NNTP-Posting-Host: ariane.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V3.2 alpha) Since many people have been interested in a LINUX version of our new alignment program, a LINUX executable of DIALIGN ******* is now available. DIALIGN is a completely novel program for pairwise as well as multiple alignment of nucleic acid and protein sequences. It is especially suited to detect local similarities in otherwise unrelated sequences and it does not employ any kind of gap penalty. The method is described in B. Morgenstern, A. Dress, T. Werner: Multiple DNA and protein sequence alignment based on segment-to-segment comparison Proc. Natl. Acad. Sci. 93 pp. 12098 - 12103 (1996) The DIALIGN executable for LINUX as well as executables for various UNIX platforms (DEC, SGI, CONVEX, HP, SUN) together with a detailed user guide, online help and a test example are available at http://www.gsf.de/biodv/dialign.html or via ftp: ftp://ariane.gsf.de/pub/unix/dialign More detailed information on DIALIGN is available at our web page. If you have any questions, comments or suggestions for improvements of the program, please feel free to contact us by e-mail. Since we plan to continue in the development of the DIALIGN program, ANY KIND OF FEEDBACK IS WELCOME! Burkhard Morgenstern ---------------------------------------------------------- Dr. Burkhard Morgenstern GSF - National Research Center for Environment and Health, Institute of Biomathematics and Biometry Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany Email: morgenstern@gsf.de From owner-software@net.bio.net Sat Mar 01 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!europa.clark.net!newsfeed.internetmci.com!news.dtinet.or.jp!ppp17!aisoai From: aisoai@agc.co.jp (ISOAI Atsushi) Newsgroups: bionet.software Subject: Re: Looking for digital image analysis software Date: Sun, 02 Mar 1997 21:06:11 +0900 Organization: Research Center, Asahi Glass Co.LTD. Lines: 30 Message-ID: References: <5f9ubd$rca@dfw-ixnews12.ix.netcom.com> NNTP-Posting-Host: ppp17.yokohama2.dtinet.or.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Newsreader: NewsWatcher-J 2.0J16 In article <5f9ubd$rca@dfw-ixnews12.ix.netcom.com>, kschap@ix.netcom.com (Kane L. Schaphorst) wrote: ..... >While I believe these imaging systems may be adequate for figure composition >and image archival, I am not certain about this. Furthermore, I do not know of >any decent freely available or commercially available software that can perform >quantitative analysis on these images. To date, the only image analysis I have >needed to perform is densitometry by either profile or volume analysis. > ..... Hi, I can not recommend the best imaging systems for your purpose, but if you have PC and scanner why not you try NIHImage. It's free but (I think) it's one of the best image software in the world. You can get it from: URL: http://rsb.info.nih.gov/nih-image/ Please try it. I hope it is useful for you. ================================================================= Atsushi Isoai, Ph.D. Senior Staff Researcher, Research Center, Asahi Glass Co.LTD. URL: http://www.yk.rim.or.jp/~aisoai/index.html ================================================================= From owner-software@net.bio.net Sat Mar 01 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!dispatch.news.demon.net!demon!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsxfer.itd.umich.edu!uunet!in1.uu.net!192.89.123.24!nntp.inet.fi!news.funet.fi!news.kbfi.ee!kadri.ut.ee!not-for-mail From: Veljo Kisand Newsgroups: bionet.software Subject: Q:cell counting software Date: Sun, 02 Mar 1997 20:28:23 +0200 Message-ID: <3319C6C7.5F14@ut.ee> Reply-To: kisand@ut.ee NNTP-Posting-Host: ppp9.hugo.ut.ee Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Lines: 11 Hi all, does anybody have some kind software for cell counts? I mean manual countig by ordinary microscope, only thing to do for software is input data, and to do so some statistics (how well data fit to probability or what ever..). I'm using dos/win3.11/win95 thanx in advance Veljo Kisand Unvi of Tartu From owner-software@net.bio.net Sat Mar 01 22:00:00 1997 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel) Newsgroups: bionet.software Subject: Re: Equation Editor Date: 2 Mar 1997 07:10:50 -0800 Organization: CNRS Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <33198C8B.52AF@ibsm.cnrs-mrs.fr> Reply-To: athel@ir2cbm.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Gerard Pujadas wrote: "Which is the best Equation Editor available for Mac (and free of course ;-) ) to make complex statistical formulas before to paste them in text." I think your demands are incompatible. If you want a free editor you'll have to put up with what is supplied with word processors like Word 6 (plus, of course the pain of having to do your word processing in Word 6). If you really want the best one available, try Expressionist, from Prsecience Corporation. It's not free, but it's a lot better than any other I've seen. I've not updated since version 2.07 (March, 1990), because that version still works perfectly with current Mac system software and more recent word processors than I was using then. Another possibility, which will give you even better results than Expressionist, at the cost of a considerable investment of effort on your part, is to learn TeX, of which good shareware implementations for Mac are available. That'll cost you little or no money, but don't imagine you'll be constructing "complex statistical formulas" the first day, though with Expressionist you would be. Athel Home page: http://ir2lcb.cnrs-mrs.fr/lcbpage/athel/home_page.html From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsxfer.itd.umich.edu!news2.acs.oakland.edu!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (Ketchup) Newsgroups: bionet.software Subject: GeneDoc 2.0.0 Released: Alignment Editor for Windows Date: Mon, 03 Mar 1997 04:02:02 GMT Organization: Concentric Internet Services Lines: 343 Message-ID: <5fdj83$qcj@chronicle.concentric.net> NNTP-Posting-Host: cnc50198.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Greetings All, Please be informed that GeneDoc version 2.0.0 has been released to GeneDoc's web site: http://www.cris.com/~ketchup/genedoc.shtml Its been 6 months since the last release, and there has been plenty of work done. Lots of internal work on the program has been done so that there are no limitation or troubles on the amount of data that can be read or displayed. Screen routines are faster and printer routines work better. New printer options, Metafile support and much improved fasta and .msf file read routines. The toolbar and shading methods are much more flexible and intuitive to use. Two major biological features have been added. Secondary Structure shading and Super Family Group support. The Secondary Structure shading routines have been built on top of a generalized User Definable set of shading routines, so you can now use GeneDoc to shade sequences any way you can imagine. File Read routines for many of the Secondary Structure prediction output files created at EMBL are built in. GeneDoc reads DSSP files, also available at EMBL. Support for files from a new database of Secondary Structure information from PSC is provided. Use the User Defined routines to shade sequences with any prediction program. GeneDoc now provides support for organizing sequences in groups and do some nifty shading based on the groups. Apply structure information to each group, do group conserved, contrast and PCR contrast shading. I've included a more complete discussion of some of the new features in GeneDoc below. Sincerely, Karl Nicholas ketchup@cris.com ----- Written by Dr. Hugh Nicholas ------- Group and Structure Features of GeneDoc. Increasingly families of genes and proteins are organized into superfamilies. Database organizations often use a the percent of residue identity as the criterion for distinguishing whether a pair of sequences should be assigned to the same family or different families within a superfamily. Perhaps a more useful criterion is whether or not a gene duplication has taken place in the common evolutionary history of the two sequences. Evolutionary biologists use this classification and refer to homologous sequences that have only speciation events and not have gene duplication events in their common evolutionary history as being orthologous. Homologous sequences that have a gene duplication event in their common evolutionary history are referred to as paralogous. Orthologous genes or proteins generally carry out the same biochemical and physiological functions while paralogous proteins generally carry out similar but related functions. For instance, mammalian myoglobins, which carry oxygen within cells are a orthologous family. They are part of a superfamily that includes the alpha hemoglobins and the beta hemoglobins, both of which are also orthologous families. These three homologous families are part of the same paralogous superfamily, as are other globin genes and proteins. Families and superfamilies can be organized around functional criteria as well as evolutionary criteria and sequence divergence. Although all sixty plus transfer RNA sequences in E. coli are paralogous with each other they can be grouped together by their twenty amino acid acceptor activities. The group functions in GeneDoc are designed to allow users to work with and analyze groups based on any of the above criteria or any user determined criteria for dividing a set of sequences into groups. The first step in working with groups is to access the groups configuration dialog. The group configuration dialog can be accessed either by selecting the "edit sequence groups" item on the groups menu or by clicking the groups button, the button marked with an upper case G on the upper toolbar. The group configuration dialog allows the user to allocate the sequences to groups and to select a color to be associated with each group. For the purposes of most of the GeneDoc group analyses sequences that are not explicitly assigned to a group will be treated as if each unassigned sequence constitutes the only member of its own group. These implicit groups will not be analyzed but the sequences will be used in the analyses of the defined groups as "other" groups and thus they will contribute to the analysis. The group analyses result in different shading for individual groups. These shadings highlight different degrees of different kinds of conservation of residues or properties within and between groups. One analysis, referred to as the Dstat analysis, measures how different the groups are from one another and whether this difference is statistically significant. The Dstat analysis presents its results as a graph and numerical values. The simplest analysis is performed by the "shade group conserved" entry on the Groups menu. This analysis highlights positions within each group that are completely conserved, that is there is only one residue at that position within the group. This highlighting is done in the color assigned to the group in the group definition dialog. This measurement of conservation within the groups does not take into account any equivalency groups, even if they are active. The second thing this analysis does is to highlight the positions that are completely conserved across all of the groups, that is there is only one residue at that position for all of the sequences in the alignment. This part of the analysis does take the equivalency groups into account if they are in effect. The final action is to compute a consensus sequence based on the entire alignment. The most useful information derived from this analysis is to identify for the user the regions of the alignment where structural or functional requirements may have been relaxed or eliminated (or alternatively added as the group evolved a new function) for some groups relative to others. For this kind of information to be reliable the conserved groups need to be both large and from a diverse range of organisms. Otherwise the observed conservation may simply be the result of a small data set with highly dependent observations. A more stringent analysis is performed by the "shade group PCR contrast" entry on the Groups menu. Sites highlighted by this analysis meet two criteria. First is that a single residue is completely conserved within the group. Second this conserved residue does not appear, at that position, in any sequence outside of the group in which it is conserved. This analysis marks unique sequence features of the group that can be useful in defining a group motif and possibly in defining a primer sequence to be used in a polymerase chain reaction (PCR) amplification of the gene. The "shade group contrast" entry on the Groups menu performs an analysis similar to that of the "shade group PCR contrast" entry. This analysis makes use of the scoring table designated for alignment scoring to divide scores for pairs of amino acids into three classes, positive, negative, and neutral. The positive scores are those that are positive numbers in the similarity scores form of the table. Similarly, the negative scores are those that are negative numbers in the similarity scores form of the table, while the neutral scores have a zero score. The scores are stored in GeneDoc as distance or dissimilarity scores and hence must be converted to the similarity form. This is done by subtracting the score for a pair of sequence residues in the table from a constant called the zero cost distance, stored with the table. Thus the largest distances become negative similarities and small distances become positive similarities. The interpretation of the scoring tables is that positive similarities are conservative substitutions and are favored over random substitutions in the evolutionary process relating the sequences. The analysis performed by the "shade group contrast" entry on the Groups menu is less restrictive about the degree of conservation within the group than is . All of the sequence residues found at a position within the group are required to have a positive similarity score with each other, and thus to be conservative substitutions. This analysis is, however, more restrictive than is the analysis performed by the "shade group PCR contrast" entry on the Groups menu when dealing with residues outside the group. The residues outside of the group must have a negative similarity score with every residue from within the group, thus they are not allowed to be either conservative or neutral substitutions. An example of using this kind of analysis to study the recognition of transfer RNAs by aminoacyl tRNA synthetase enzyme can be found in McClain and Nicholas, 1987. Nicholas et al., 1987 describes using the contrasts to plan site directed mutagenesis experiments to confirm the analysis of the tRNAs. The analysis called the Dstat analysis is the Kolmogorov-Smirnov test for the equality of two distributions. The Dstat analysis is accomplished by first selecting a region (or all) of the alignment for use in the test calculations. Then you can either select the analysis under the Dstat menu or click the Dstat tool bar button. The Dstat toolbar button is near the right end of the upper toolbar and is marked by a pair of "S" shaped curves representing the cumulative distributions used in the test. As noted above, the Dstat analysis is a statistical test of whether the groups defined by the user are significantly different from each other. The first step in the test is to compute an alignment score for each pair of sequences over the region selected by the user. These scores are the partitioned into two distributions. The first distribution is composed entirely from scores where both of the sequences used to compute the score are members of different user defined groups. This is called the between groups distribution. The second distribution is composed entirely from scores where both of the sequences used to compute the score are members of the same user defined group. Note that this includes scores from every group with two or more sequences. This distribution is called the within groups distribution. These two distributions are plotted as cumulative distributions. That is the score is plotted versus the fraction of the scores in the distribution that are less than or equal to the score being plotted. The Kolmogorov-Smirnov D statistic (Dstat) is the maximum difference between the two distributions (along the fractional axis). Recent advances in the understanding of the distribution of values taken on by Dstat allow us to compute its one-sided significance probability. The one-sided significance probability is used rather than the two-sided significance probability because we are only interested in the case where the between groups distribution is composed of larger scores than the within groups distribution. The other situation, where the within groups distribution is composed of larger scores than the between groups distribution corresponds to either convergent evolution or some sort of selection in favor of divergence, situations that are not usually part of the hypothesis. The Kolmogorov-Smirnov test was selected instead of the more common Student’s t test or the F test because it is sensitive to both the location of the distributions along the scores axis and to the shape of the distribution. Student’s t test is sensitive to only the location of the distributions and the F test is sensitive only to differences in the variance of the distribution, only one of several aspects affecting the shape of the distributions. Thus the Kolmogorov-Smirnov test can find the distributions to be different when either Student’s t test or the F test might have failed. Because of this it is necessary for the user to examine the plot carefully to determine the exact nature of the differences in the two distributions being tested. The user should exercise care that the biological hypothesis being examined should lead to the type of difference actually observed. Examples of testing biological hypotheses with sequence data and the Kolmogorov-Smirnov test can be found in Nicholas and Graves, 1983 and in Nicholas and McClain, 1995. The Nicholas and Graves paper contains an extended discussion of formulating Kolmogorov-Smirnov tests that correspond to different kinds of biological hypotheses. The structure groups and shading facility provide an extremely powerful and flexible set of tools for integrating sequence information with structural information. The facility is flexible enough to allow the user to display almost any kind of information as color codes along the sequence. Such states can include the obvious secondary structure state of the residue in the three dimensional structure. Less obvious properties like the solvent accessible surface area of the residue or its side chain can also be displayed. The fraction of the side chain in a polar environment is another characteristic that is sometime informative. One of the most powerful kinds of integration of structure and sequence information allows the user to visually examine the variation in structure or some structural property that occurs as the sequence varies in a series of homologous proteins. This same display allows the user to adjust the alignment based on information derived from the varying structures of a series of homologous proteins. Alternatively, you can have several copies of the same sequence in the alignment by adding additional copies with different names through the sequence import facility. Remember that each copy must have its own distinct name. These copies of the same sequence can all be highlighted using a different property. This allows you to easily visualize possible correlation of properties or of properties with sequence or structure. Another use for multiple copies of a single sequence in the alignment is to contrast predictions of structure and properties with that observed in an experimentally determined three dimensional structure. A wide spread use of the structure shading is to project the structure or properties from a sequence of known structure onto sequences whose structures have not be experimentally determined. This is accomplished by combining the structure shading facility with the group facility. At the same time you use the structure shading dialogue to associate a structure file with a specific sequence in the alignment you can designate that sequence as the master sequence of a structural group. This allows you to associate several sequences with a single structure file. These associated sequences will be shaded with the same colors in the same column of the alignment as the master sequence regardless of the sequence residue present in thhat position of the sequence. Thus this is essentially a low resolution homology modeling facility. All of these features can be combined into a very informative display for studying structure-function relationships in the following procedure. First, associate a structure file with each sequence in your alignment whose structure has been determined by X-ray crystallography or NMR. Make these sequences the master sequence for a group of the most closely related sequences in the alignment. Ideally the sequences within each group should have common biochemical properties such as substrate specificity, while different groups can have different substrate specificities. Use the sequence editing facility to put sequences in the same group on adjacent rows of the alignment. Put the group master sequence at the top of each group. Then set the display mode to differences mode and make sure this is applied to all of the groups. This yields a display with all of the group master sequences, that is the sequences with known structures, displayed with all of their residues. The other sequences in each group have a dot displayed where they have the same sequence residue as the group master. Sequence residues that are different from the group master sequence are shown. This highlights substitutions within each group that are presumably successful site directed mutagenesis experiments performed by nature. Differences between groups may be associated with the change in substrate specificity or other property. It can be very helpful to have exactly the same alignment in a second window highlighted in group contrast mode. This combination of displays can be a very powerful tool for examining structure-function relationships by integrating a large amount of information in an easy to comprehend format and presentation. Nicholas, H.B. Jr., and Graves, S.B. 1983. Clustering of transfer RNA by cell type and amino acid specificity. Journal of Molecular Biology, vol. 171, pp. 111 - 118. Nicholas, H.B., Jr., Chen, Y-M., and McClain, W.H. 1987. Comparisons of transfer RNA sequences. Computer Applications in the Biosciences, vol. 3, p. 53. McClain, W.H. and Nicholas, H.B,Jr. 1987. Discrimination between transfer RNA molecules. Journal of Molecular Biology, vol. 194, pp. 635 - 642. Nicholas, H.B. Jr. and McClain, W.H. 1987. An algorithm for discriminating transfer RNA sequences. Computer Applications in the Biosciences, 3, pp. 177 - 181. Nicholas, H.B. Jr. and McClain, W.H. 1995. Searching tRNA Sequences for Relatedness to Aminoacyl tRNA Synthetase Families. Journal of Molecular Evolution, vol. 40, pp. 482-486. From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!ix.netcom.com!news From: CLARENCE JOSEPH WILSON, JR. Newsgroups: bionet.software Subject: earn extra cash!!! Date: Mon, 03 Mar 1997 03:34:30 GMT Organization: Netcom Lines: 3 Message-ID: <5fdgko$7m1@dfw-ixnews12.ix.netcom.com> NNTP-Posting-Host: nor-la5-15.ix.netcom.com X-NETCOM-Date: Sun Mar 02 9:30:32 PM CST 1997 X-Newsreader: NETCOMplete/3.0 earn extra cash from your computer at home. send me your email address and I'll tell you how. send to mrzu666@ix.netcom.com From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: Chromas 1.4 Date: Mon, 03 Mar 1997 13:30:59 +1000 Organization: Griffith University Lines: 24 Message-ID: <331A45F3.2426@sct.gu.edu.au> NNTP-Posting-Host: ibeacham.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; 68K) Hi, Chromas is a free Windows application which displays and prints chromatogram files in ABI and Staden SCF format. It allows basecall editing and exporting of the sequence to a file or the clipboard. It also features reverse/complement and search functions. There are versions for Windows 3.1 and Windows 95. New in version 1.4: - The backspace key now deletes backwards instead of forwards (woops!). - There is now an option to find the next occurrence of an "N" in the sequence. - Multiple files can be selected in the Open dialog box. New windows are created for the files. - You can zoom in up to 64X on the Y-axis. Chromas can be downloaded from: http://trishul.sci.gu.edu.au/~conor/chromas.html Cheers, Conor From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!news.mtu.edu!msunews!not-for-mail From: ~{:C3TWl~} <"~{:C3TWl~}"@~{D31#C\\5%N;~}.edu> Newsgroups: bionet.software Subject: test Date: Mon, 03 Mar 1997 10:30:26 -0600 Organization: ~{D31#C\5%N;~} Lines: 1 Sender: -Auth- @port15.ts1.msstate.edu Message-ID: <5feu97$ish$1@msunews.cl.msu.edu> Reply-To: "~{:C3TWl~}"@~{D31#C5%N;~}.edu NNTP-Posting-Host: port15.ts1.msstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-AUTHid: chenglia X-Mailer: Mozilla 3.01Gold (Win95; I) test From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!msunews!netnews.upenn.edu!XAVIER!news.drexel.edu!dunx1!sg928ah5 From: sg928ah5@dunx1.ocs.drexel.edu (James Ianni) Newsgroups: bionet.software Subject: Web page for Kintecus... Date: 3 Mar 1997 00:04:49 GMT Organization: Drexel University Lines: 7 Message-ID: <5fd4j1$9kp@noc2.drexel.edu> NNTP-Posting-Host: dunx1.ocs.drexel.edu X-Newsreader: TIN [version 1.2 PL2] A web page has been created for Kintecus, "The Kinetics Program for the Ultimate Lazy Scientist". It contains some info and pictures, graphs. Point your browser to: http://httpsrv.ocs.drexel.edu/grad/sg928ah5 From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Newsgroups: bionet.molec-model,comp.windows.x.apps,comp.graphics.visualization,bionet.software Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!friedric From: friedric@techfak.uni-bielefeld.de (Friedrich Ackermann) Subject: Re: C/C++ molec.modelling graphics libs. ?? Message-ID: Sender: friedric@TechFak.Uni-Bielefeld.DE (Friedrich Ackermann) Date: Mon, 3 Mar 1997 10:06:03 GMT References: <5f3u4n$98s@falcon.le.ac.uk> <5f48p4$le@vixen.cso.uiuc.edu> Nntp-Posting-Host: puccini.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 45 Xref: biosci bionet.molec-model:1413 comp.windows.x.apps:13201 comp.graphics.visualization:9576 bionet.software:18023 In article <5f48p4$le@vixen.cso.uiuc.edu>, dalke@ks.uiuc.edu (Andrew Dalke) writes: |> nsr2 asked about: |> > shareware molecular modelling graphics libraries written in C or C++ to |> > run on UNIX - Xwindows (SUN or SG)?? |> ... |> |> It really just depends. For instance, I would prefer a multi- |> language solution mixing C++ and Fortran (perhaps with a bit of Python |> or Tcl to glue it all together). Others will and do disagree with |> me, but I've found the mixed C++/Tcl model for VMD to be quite |> useful and powerful. |> I agree. Our visualisation server "viwish" also has been build mixing C and Tcl/Tk. I can recommend such a solution. You may confere http://www.TechFak.Uni-Bielefeld.DE/techfak/ags/ai/viwish-home/ or @article{klein96, author = {Klein, T. and Ackermann, F. and Posch, S.}, title = {viwish: A visualisation server for protein modelling and docking}, journal = {Gene--COMBIS}, year = {1996}, volume = {Gene 183}, number = {}, pages = {GC51-GC58}, keywords = {Visualisation, protein structure, Tcl, Tk, TclTk, rendering, molecular graphics} }. ------------------------------------------- Friedrich Ackermann Technical Faculty Bielefeld University P.O. Box 100131 D-33501 Bielefeld Phone: +49 521 106 2938 (2935) Fax: +49 521 106 2992 email: friedric@techfak.uni-bielefeld.de http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/friedric/ ------------------------------------------- From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!newsxfer.itd.umich.edu!uunet!in2.uu.net!194.163.252.65!news.maz.net!news.is-europe.net!news.gni.net!rnima!gunhill.swb.de!reish Date: 01 Mar 1997 21:51:00 +0100 From: reish@gunhill.swb.de (Harry Reis) Newsgroups: bionet.software Message-ID: <6S3oRBZN0LB@gunhill.swb.de> Subject: Search IPG-Calculator X-Newsreader: CrossPoint v3.11 R/C1234 Lines: 17 Message written on 01.03.97 at 21:48 Hi, does somebody now a ftp-address where I can find a program to calculate the recipes for different immobiline gradients. As far as I know there is a program called "gradient-maker" or so. ... see you later aligator Harry From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel) Newsgroups: bionet.software Subject: Re: Equation Editor Date: 2 Mar 1997 23:49:13 -0800 Organization: CNRS Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <331A767F.B44@ibsm.cnrs-mrs.fr> Reply-To: athel@ir2cbm.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Ken Brady asked: "Could you please tell me how to contact Prsecience Corporation." In 1990 their address was Prescience Corporation 939 Howard Street San Francisco, California 94103 USA Telephone +1 415 543 2252 AppleLink DO588 Whether any of this still applies I don't know. (That's why I didn't put it in my message of yesterday). Athel Home page: http://ir2lcb.cnrs-mrs.fr/lcbpage/athel/home_page.html From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!mcimail.com!POSTMASTER From: POSTMASTER@mcimail.com (POSTMASTER) Newsgroups: bionet.software Subject: MCI Mail Message Reject Notice Date: 3 Mar 1997 13:10:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 55 Sender: daemon@net.bio.net Distribution: world Message-ID: <97030321123189.POSTMASTERDC6EM@MCIMAIL.COM> NNTP-Posting-Host: net.bio.net -----------------MCI Mail Internet Gateway Service Message------------------ Message Rejection Time: 21:12:31 GMT, Mon 3 MAR 1997 Status: Message COULD NOT be Posted into MCI Mail Message Information: From: EMS: Internet MBX: bio-soft@net.bio.net Subject: CorelDraw 7! only costs US$40?! Shopping Paradise Reason(s) for Rejection: Message Sender Address was invalid. 626 Data is required following the specified field 626 Data is required following the specified field FROM: EMS: MBX: Additional Message Information: ------------------------------ Received: from gatekeeper2.mcimail.com by mailgate5.mcimail.com id aa06793; 3 Mar 97 21:11 WET Received: from fc.mcimail.com by gatekeeper.mcimail.com (PMDF V5.0-8 #16706) id <0E6HK5I070004P@gatekeeper.mcimail.com> for 0004536233@mcimail.com; Mon, 03 Mar 1997 21:10 +0000 (GMT) Received: from net.bio.net (204.31.212.2) by gatekeeper.mcimail.com (PMDF V5.0-8 #16706) id <0E6HK58B900N68@gatekeeper.mcimail.com> for 0004536233@mcimail.com; Mon, 03 Mar 1997 21:10 +0000 (GMT) Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id MAA19755; Mon, 03 Mar 1997 12:55:44 -0800 Received: (from news@localhost) by net.bio.net (8.6.12/8.6.6) id MAA19734; Mon, 03 Mar 1997 12:55:43 -0800 Date: Fri, 28 Feb 1997 22:44:12 +0000 (GMT) From: Subject: CorelDraw 7! only costs US$40?! Shopping Paradise To: bio-soft@net.bio.net Message-id: <5f5vh8$bga@imsp009a.netvigator.com> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT NNTP-posting-host: dialh09188.netvigator.com X-Newsreader: Forte Agent .99b.112 ------------------------------------------------------------------------------ From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!howland.erols.net!vixen.cso.uiuc.edu!ks.uiuc.edu!dalke From: dalke@ks.uiuc.edu (Andrew Dalke) Newsgroups: bionet.software Subject: Re: Software for 3-D graphics! Date: 3 Mar 1997 17:31:24 GMT Organization: TB BI Lines: 20 Distribution: world Message-ID: <5ff1tc$n2k@vixen.cso.uiuc.edu> References: <5fdjkl$cmc$1@news.cc.umr.edu> NNTP-Posting-Host: ophelia.ks.uiuc.edu Raghavender Pillutla asked: > Can anyone tell me where I can find a software that can display simple > objects in 3-D? Specifically, I want to know if there is any programs > which can display spheres when I give the radius and the x,y,z > coordinates of the center. You might try AtomTV. See http://www.hprc.utoronto.ca/HPRC/visualization/examples/atomtv/doc/atomtv.html However, it looks like it only works for SGIs, and you posted from an HP, so you might want try PlotAtoms from the LASSP Tools distribution at http://www.lassp.cornell.edu/LASSPTools/LASSPTools.html . It says: > For example, it's currently an incredible pain to plot spheres on your > screen. We've cured this with PlotAtoms. Seems to fit your situation, though it doesn't appear obvious on how to set the sphere radius for each term. Andrew dalke@ks.uiuc.edu From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.sgi.com!mr.net!newsfeed.direct.ca!newsgate.direct.ca!usenet From: pnorrish@direct.ca (Paul Norrish) Newsgroups: bionet.software Subject: download my handy little address book and phone dialer for windows Date: 3 Mar 1997 17:11:05 GMT Organization: PM Enterprises Lines: 9 Message-ID: <5ff0n9$gbj$2@orb.direct.ca> NNTP-Posting-Host: van-as-08b06.direct.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 wrote an addess book and phone dialer for windows,its really good and simple.you can download the demo off my homepage at " http://mypage.direct.ca/p/pnorrish/ " or at " http://www.axxis.com/altus/products.html " It's called "my litle address book " by PM Enterprises Paul Norrish From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!newsfeeds.sol.net!mr.net!newsfeed.direct.ca!newsgate.direct.ca!usenet From: pnorrish@direct.ca (Paul Norrish) Newsgroups: bionet.software Subject: download my handy little address book and phone dialer for windows Date: 3 Mar 1997 17:12:29 GMT Organization: PM Enterprises Lines: 9 Message-ID: <5ff0pt$gbj$3@orb.direct.ca> NNTP-Posting-Host: van-as-08b06.direct.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 wrote an addess book and phone dialer for windows,its really good and simple.you can download the demo off my homepage at " http://mypage.direct.ca/p/pnorrish/ " or at " http://www.axxis.com/altus/products.html " It's called "my litle address book " by PM Enterprises Paul Norrish From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!demos!news-out.communique.net!news.ultranet.com!not-for-mail From: Ken Brady Newsgroups: bionet.software Subject: Re: Equation Editor Date: Mon, 3 Mar 1997 02:16:42 GMT Organization: UltraNet Communications, Inc. Lines: 31 Message-ID: <5fdbue$bb5$1@decius.ultra.net> References: <33198C8B.52AF@ibsm.cnrs-mrs.fr> NNTP-Posting-Host: kbrady.ultranet.com X-Newsreader: Post Road News Reader 1.2 > > Gerard Pujadas wrote: > > "Which is the best Equation Editor available for Mac (and free of course > ;-) ) to make complex statistical formulas before to paste them in > text." > > I think your demands are incompatible. If you want a free editor you'll > have to put up with what is supplied with word processors like Word 6 > (plus, of course the pain of having to do your word processing in Word > 6). If you really want the best one available, try Expressionist, from > Prsecience Corporation. It's not free, but it's a lot better than any > other I've seen. I've not updated since version 2.07 (March, 1990), > because that version still works perfectly with current Mac system > software and more recent word processors than I was using then. > > Another possibility, which will give you even better results than > Expressionist, at the cost of a considerable investment of effort on > your part, is to learn TeX, of which good shareware implementations for > Mac are available. That'll cost you little or no money, but don't > imagine you'll be constructing "complex statistical formulas" the first > day, though with Expressionist you would be. > > Athel Could you please tell me how to contact Prsecience Corporation. Thanks! Ken Brady kbrady@ultranet.com From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!newsxfer.itd.umich.edu!news.flint.umich.edu!news.gmi.edu!msunews!not-for-mail From: ~{:C3TWl~} <"~{:C3TWl~}"@~{1#C\\5%N;~}.edu> Newsgroups: bionet.software Subject: Re: test Date: Mon, 03 Mar 1997 10:32:56 -0600 Organization: ~{D31#C\5%N;~} Lines: 4 Sender: -Auth- @port15.ts1.msstate.edu Message-ID: <5feudr$isi$1@msunews.cl.msu.edu> References: <5feu97$ish$1@msunews.cl.msu.edu> Reply-To: "~{:C3TWl~}"@~{1#C5%N;~}.edu NNTP-Posting-Host: port15.ts1.msstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-AUTHid: chenglia X-Mailer: Mozilla 3.01Gold (Win95; I) ~{:C3TWl~} wrote: > > test test From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!news.starnet.net!news.starnet.net!news.missouri.edu!usenet.umr.edu!not-for-mail From: Raghavender Pillutla Newsgroups: bionet.software Subject: Software for 3-D graphics! Date: 3 Mar 1997 04:21:41 GMT Organization: UMR Missouri's Technological University Lines: 8 Message-ID: <5fdjkl$cmc$1@news.cc.umr.edu> NNTP-Posting-Host: saucer.cc.umr.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA release 970114] Hello, Can anyone tell me where I can find a software that can display simple objects in 3-D? Specifically, I want to know if there is any programs which can display spheres when I give the radius and the x,y,z coordinates of the center. Pl. help. thanks in advance. Raghu From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!newspump.sol.net!howland.erols.net!ais.net!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (Ketchup) Newsgroups: bionet.software Subject: Re: Gene fusion by PCR Date: Mon, 03 Mar 1997 04:12:13 GMT Organization: Concentric Internet Services Lines: 27 Message-ID: <5fdjr4$t@chronicle.concentric.net> References: <5f1tl2$3jl@rc1.vub.ac.be> NNTP-Posting-Host: cnc50198.concentric.net X-Newsreader: Forte Free Agent 1.0.82 GeneDoc has facilities for analyzing subsets of the sequences in a protein multiple sequence alignment for their potential as PCR sites. It identifies positions in the alignment where all of the amino acids within the subset being analyzed are identical and do not appear in any of the sequences outside of the subset. There are user selectable options that let you define a small group of amino acids to treat as in they were a single amino acid in the analysis. http://www.cris.com/~ketchup/genedoc.shtml ldewit@ben.vub.ac.be (mbraiban) wrote: >Does anybody know a software that could assist me in designing primers >for PCR recombination? >Dimitri Harmegnies >Dept. of Virology >Institut Pasteur de Bruxelles >642 rue Engeland >B-1180 >Brussels, Belgium From owner-software@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!news.mtu.edu!msunews!netnews.upenn.edu!taurus.fccc.edu!sauder From: sauder@castor.fccc.edu (John Michael Sauder) Newsgroups: bionet.software Subject: Re: Looking for digital image analysis software Date: 3 Mar 1997 16:47:49 GMT Organization: Fox Chase Cancer Center, Philadelphia, PA Lines: 33 Message-ID: <5fevbl$1pt@taurus.fccc.edu> References: <5f9ubd$rca@dfw-ixnews12.ix.netcom.com> NNTP-Posting-Host: castor.rm.fccc.edu In article aisoai@agc.co.jp (ISOAI Atsushi) writes: >In article <5f9ubd$rca@dfw-ixnews12.ix.netcom.com>, kschap@ix.netcom.com >(Kane L. Schaphorst) wrote: > >..... > >> While I believe these imaging systems may be adequate for figure >> composition and image archival, I am not certain about this. Furthermore, >> I do not know of any decent freely available or commercially available >> software that can perform quantitative analysis on these images. To date, >> the only image analysis >>needed to perform is densitometry by either profile or volume analysis. > >Hi, >I can not recommend the best imaging systems for your purpose, >but if you have PC and scanner why not you try NIHImage. >It's free but (I think) it's one of the best image software in >the world. You can get it from: >URL: http://rsb.info.nih.gov/nih-image/ >Please try it. I hope it is useful for you. >Atsushi Isoai, Ph.D. NIH-Image runs on the Mac. There was a beta version of a port to the PC called Scion Image, I think. There's also a program called ImageTool. Check out these URLs: http://ddsdx.uthscsa.edu/dig/itdesc.html http://rsb.info.nih.gov/nih-image/default.html Both these programs can do densitometry. -- -- Mike S. (M_Sauder@fccc.edu) http://www.fccc.edu/research/labs/roder/mike/ From owner-software@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!axe.netdoor.com!not-for-mail From: mbc1954@netdoor.com (Michael) Newsgroups: bionet.software Subject: Re: Growth Rate Animation - wanted! Date: Mon, 03 Mar 1997 22:29:24 GMT Organization: Internet Doorway, Inc. http://www.netdoor.com Lines: 31 Message-ID: <331b507e.781476@news.netdoor.com> References: <3319eba3.3532285@news.netdoor.com> NNTP-Posting-Host: port88.hat.netdoor.com X-Newsreader: Forte Free Agent 1.1/32.230 On Sun, 02 Mar 1997 21:07:02 GMT, mbc1954@netdoor.com (Michael) wrote: E-mail address is Chris282@AOL.Com ---changed from cmc282@aol.com >Your Assistance is Requested! > >I am a ninth grade biology student completing a project on the use of >math and computers to model bacteria growth. > >I have completed my laboratory phase and cultured E. Coli on blood >agar plates, observed colony growth and counted the colonies at hourly >intervals. > >I then formulated a growth rate and projected the growth curve for a >24 hour period. > >What I need is an animation program to help visualize that growth >using a time-compressed animation. I have a slide show that uses the >hourly observations, but it is fairly primative and does not use the >calculated growth rate (just static graphics is a slide show format.) > >I know that this 'real math' animation can be done, but I have neither >the math or programming skills ( nor time to learn before the project >deadline) to do it through QBasic. > >Any suggestions or advice would be appreciated. Pentium-based, Win95 >system. > >Chris Cruthird >CMC282@AOL.COM From owner-software@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!quagga.ru.ac.za!ru.uni.net.za!und.uni.net.za!und.ac.za!newsadmin From: Rob Miller Newsgroups: bionet.software Subject: Re: Software for 3-D graphics! Date: Tue, 04 Mar 1997 09:41:05 +0000 Organization: South African National Bioinformatics Institute Lines: 34 Message-ID: <331BEE31.50D2E2A5@house.med.und.ac.za> References: <5fdjkl$cmc$1@news.cc.umr.edu> NNTP-Posting-Host: house.med.und.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; Linux 1.3.86 i586) Raghavender Pillutla wrote: > > Hello, > > Can anyone tell me where I can find a software that can display simple > objects in 3-D? Specifically, I want to know if there is any programs > which can display spheres when I give the radius and the x,y,z > coordinates of the center. Pl. help. thanks in advance. > > Raghu I believe you can do this with Roger Sayle's RasMol (free), though you will have to put your xyz coords into something that looks like a PDB (Brookhaven Protein Data Bank) file with the radius where the R-factor goes. rob. -- ---------------------------------------------------------------------------- Robert T. Miller, Ph.D. rmiller@house.med.und.ac.za Manager - Durban Satellite - South African National Bioinformatics Institute Faculty of Medicine / Dept of Virology / University of Natal Private Bag 7 / Congella 4013 / Durban / South Africa phone +27 (031) 3603743 fax +27 (031) 3603744 or 2604441 ---------------------------------------------------------------------------- From owner-software@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!LAMAR.COLOSTATE.EDU!medford From: medford@LAMAR.COLOSTATE.EDU (June Medford) Newsgroups: bionet.software Subject: Gel Pro software Date: 4 Mar 1997 12:26:20 -0800 Organization: Colorado State University Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <331C854E.2847@lamar.colostate.edu> Reply-To: medford@lamar.colostate.edu NNTP-Posting-Host: net.bio.net Hi Folks, We are interested in purchasing gel-analysis software and would appreciate your comments on the Gel Pro software from Media Cybernectics. For example, we are very concerned that this software will not integrate. How much of a problem has this been to real users? thanks in advance, June Medford -- ******************************************* Dr. June Medford Department of Biology Colorado State University Fort Collins, CO 80523-1878 Telephone:(970)-491-7865 office (970)-491-3991 laboratory FAX:(970)-491-0649 EMAIL: medford@lamar.colostate.edu From owner-software@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.idt.net!cdc2.cdc.net!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: GeneDoic 2.0.1 released: Alignment Editor/Shading for Windows. Date: Tue, 04 Mar 1997 17:30:50 GMT Organization: Concentric Internet Services Lines: 20 Message-ID: <5fhm35$cep@chronicle.concentric.net> NNTP-Posting-Host: cnc502117.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Greetings All, Please be informed that GeneDoc version 2.0.1 has been released to GeneDoc's web site: http://www.cris.com/~ketchup/genedoc.shtml *** Made *** a bug at the last minute where Fasta Files could not be read into a new project. My sincerest appologies to the 100 or so of you that have downloaded it already. If you don't work with fasta files, no hurry. Karl Nicholas. Ketchup@cris.com From owner-software@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!axe.netdoor.com!not-for-mail From: mbc1954@netdoor.com (Michael) Newsgroups: bionet.software Subject: Growth Rate Animation - wanted! Date: Sun, 02 Mar 1997 21:07:02 GMT Organization: Internet Doorway, Inc. http://www.netdoor.com Lines: 26 Message-ID: <3319eba3.3532285@news.netdoor.com> NNTP-Posting-Host: port34.hat.netdoor.com X-Newsreader: Forte Free Agent 1.1/32.230 Your Assistance is Requested! I am a ninth grade biology student completing a project on the use of math and computers to model bacteria growth. I have completed my laboratory phase and cultured E. Coli on blood agar plates, observed colony growth and counted the colonies at hourly intervals. I then formulated a growth rate and projected the growth curve for a 24 hour period. What I need is an animation program to help visualize that growth using a time-compressed animation. I have a slide show that uses the hourly observations, but it is fairly primative and does not use the calculated growth rate (just static graphics is a slide show format.) I know that this 'real math' animation can be done, but I have neither the math or programming skills ( nor time to learn before the project deadline) to do it through QBasic. Any suggestions or advice would be appreciated. Pentium-based, Win95 system. Chris Cruthird CMC282@AOL.COM From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!news.mathworks.com!news.pbi.net!news.nothingbutnet.net!news.zNET.com!not-for-mail From: Raja Elhayek Newsgroups: bionet.molec-model,comp.windows.x.apps,comp.graphics.visualization,bionet.software Subject: Re: C/C++ molec.modelling graphics libs. ?? Date: Tue, 04 Mar 1997 19:50:44 +0000 Organization: zNET Internet Services Lines: 30 Message-ID: <331C7D14.44A8@sd.znet.com> References: <5f3u4n$98s@falcon.le.ac.uk> NNTP-Posting-Host: sdts1-37.znet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Xref: biosci bionet.molec-model:1420 comp.windows.x.apps:13218 comp.graphics.visualization:9604 bionet.software:18043 nsr2 wrote: > > Could someone please point me in the right direction to where I can get > shareware molecular modelling graphics libraries written in C or C++ to > run on UNIX - Xwindows (SUN or SG)?? The libraries should allow me > to display the molecules as well as providing calls to the mouse for > manipulating the model. > > I have come across sites possesing molecular modelling packages written > in fortran that comes with source code. However I am having great > difficulty finding any that are available in C or C++. > > Would it be worthwile to develop molecular modelling software in > FORTRAN, since the source code for such packages appears to be more > readily available ?? > > This request for information is purely for academic purposes (as part > of a PhD project) and would be grateful for any help/ pointers that > anyone can give me. Thanks very much > > Nithin > > nsr2@le.ac.uk Try the Molecular Graphics Visualisation tool (RasMol 2.5) you can get it from Glaxo Research & Development, UK with its manual and full C code it runs on different platforms and you can manipulate the model with the mouse. It is free. Raja From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Computational Molecular Biology Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.proteins Subject: US-NC Bioinformatics - Sequence Analysis Position Date: 4 Mar 1997 21:51:00 -0800 Organization: The University of North Carolina at Chapel Hill Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software.gcg:2261 bionet.software:18044 bionet.molbio.proteins:10164 The University of North Carolina at Chapel Hill has an immediate opening for a specialist in nucleic acid and protein sequence analysis to provide a leadership role in supporting the community of several hundred users of biocomputational tools. The successful candidate will organize courses for users, prepare documentation, and assist individual users with their sequence analysis problems. Development of publishable teaching materials or articles will be encouraged. Strong knowledge of DNA and protein sequence analysis algorithms and software is essential. Teaching experience and a background in laboratory molecular biology are highly desirable. The position requires excellent oral and written communication skills. Salary is in the range of $33-38K depending on the experience of the applicant. The University of North Carolina is an Equal Opportunity Employer. Applications or additional questions about this position may be sent via regular or email to: Philip Carl, Chair of the Search Committee 101 MBBRL, CB7100 UNC Medical School Chapel Hill, NC 27599-7100 Phone: (919)-966-3544 Fax: 919-966-6821 ====================================================================== Computational Resource for Molecular Sciences and Biotechnology at UNC http://mmlin4.pha.unc.edu/~cmb96/ From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!NINJA.LIFE.UIUC.EDU!studier From: studier@NINJA.LIFE.UIUC.EDU (Jim Studier) Newsgroups: bionet.software Subject: program "OOPSEG" needed Date: 4 Mar 1997 17:38:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <331CCEDD.15A8@ninja.life.uiuc.edu> NNTP-Posting-Host: net.bio.net I am looking for a program with the acronym OOPSEG. I takes a time series and separates it into a smooth part and a noise part. It requires that the noise part satisfy certain tests for randomness. If it is not satisfied that the noise is random it tries again. It uses something called optimal segments to do this. I have seen one paper on it. The author is David C. Bradley. I would like to know an email address or better yet a www site where I can get this program. Jim Studier (studier@ninja.life.uiuc.edu) From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-feed1.bbnplanet.com!nih.gov!usenet From: bernard@elsie.nci.nih.gov (Bernard Murray) Newsgroups: bionet.software Subject: Re: Growth Rate Animation - wanted! Date: 4 Mar 1997 23:53:50 GMT Organization: National Institutes of Health, Bethesda, MD Lines: 48 Message-ID: <5ficme$ebt@light.nih.gov> References: <3319eba3.3532285@news.netdoor.com> NNTP-Posting-Host: ermintrude.nci.nih.gov X-Newsreader: WinVN 0.99.7 In article <3319eba3.3532285@news.netdoor.com>, mbc1954@netdoor.com says... > >Your Assistance is Requested! >I am a ninth grade biology student completing a project on the use of >math and computers to model bacteria growth. >I have completed my laboratory phase and cultured E. Coli on blood >agar plates, observed colony growth and counted the colonies at hourly >intervals. >I then formulated a growth rate and projected the growth curve for a >24 hour period. >What I need is an animation program to help visualize that growth >using a time-compressed animation. I have a slide show that uses the >hourly observations, but it is fairly primative and does not use the >calculated growth rate (just static graphics is a slide show format.) >I know that this 'real math' animation can be done, but I have neither >the math or programming skills ( nor time to learn before the project >deadline) to do it through QBasic. >Any suggestions or advice would be appreciated. Pentium-based, Win95 >system. >Chris Cruthird >CMC282@AOL.COM One possibility is to convert the images to GIF files and then make a composite GIF89 image - this has all the information needed for "flickbook" animations. I believe the delay between images can be adjusted to suit each time point. Netscape has the capacity for displaying GIF89 files as animations. For creating the files under PC/Win I suggest GIF Construction Kit which is shareware ($20) and can be grabbed from http://www.mindworkshop.com As long as you don't have too many images or they are not too big or have too much colour depth the animation will proceed pretty smoothly. The file creation is point'n'click so you don't have to learn programming - just how GIF files are structured. I have used this to create animations of molecular movements using images saved from RasMol and the results are acceptable (to me). If you ever run Linux on your PC (recommended) there are some unix utilities for merging GIF files to make animated GIF89's and the results look very nice with an X file viewer. I hope that this helps. Good luck, Bernard [No affiliation with the producers of GIFCon but a happy user] Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!super.zippo.com!zdc!enews.sgi.com!news.sgi.com!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!wap18.zi.biologie.uni-muenchen.de!strimmer From: Korbinian Strimmer Newsgroups: bionet.software Subject: PUZZLE 3.0 available Date: Wed, 5 Mar 1997 14:00:13 +0100 Organization: [posted via] Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 60 Distribution: world Message-ID: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII P U Z Z L E Maximum likelihood analysis for nucleotide and amino acid alignments Version 3.0 March 1997 Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany PUZZLE is an application to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm (quartet puzzling) that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Rate heterogenity (invariable sites plus Gamma distributed rates) is incorporated in all models of substitution available (nucleotides: TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model parameters including rate heterogeneity can be estimated from the data by maximum likelihood. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of internal branches without computing an overall tree. PUZZLE is available free of charge from http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html and ftp://ftp.ebi.ac.uk/pub/software/ (archives will be updated soon) The online manual can be viewed at http://www.zi.biologie.uni-muenchen.de/~strimmer/manual.html PUZZLE is written as an ANSI C program. This means that it will run on most personal computers and workstations if compiled by an appropriate C compiler. Precompiled executables are available for MacOS and MS-DOS. UNIX and VMS makefiles are also provided. What's new in PUZZLE 3.0: * Rate heterogenity included in all models of substitution (Gamma distribution plus invariable sites). * Likelihood mapping analysis with Postscript output. * Much more sophisticated maximum likelihood parameter estimation for all model parameters including those of rate heterogenity. * Codon positions selectable. Update to mtREV24. Less verbose runtime messages. HTML documentation. Better internal error classification. More information in outfile (number of constant postions etc.). From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: James McInerney Newsgroups: bionet.software Subject: Re: recombination-detection-program Date: 5 Mar 1997 09:32:07 -0000 Organization: The Natural History Museum Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fjein$cg9@mserv1.dl.ac.uk> References: <973501653.~INN-EWPa00202.bionet-news@dl.ac.uk> Reply-To: J.McInerney@nhm.ac.uk MIME-Version: 1.0 Original-To: Holger Averdunk Holger Averdunk wrote: > > Does anyone know of software which detects recombination/gene conversion in a set of (aligned) DNA/RNA/AA sequences ? Holger Averdunk > holger@hercules.anu.edu.au The bootscanning software in conjunction with the PHYLIP package proposes to do this. Unfortunately, detecting recombination sites is just about one of the most difficult things to prove. You can get the bootscanning software at: http://hivgenome.hjf.org/ regards, James -- ========= James O. McInerney email: J.mcinerney@nhm.ac.uk Senior Scientific Officer, phone: +44 171 938 9247 Department of Zoology, Fax: +44 171 938 9158 The Natural History Museum, Cromwell Road, London SW7 5BD. ========= From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software Subject: ANNOUNCE: DBWatcher 2.00 stable + HTML doc + survey Date: Wed, 05 Mar 1997 10:32:56 +0100 Organization: IGBMC Lines: 82 Message-ID: <331D3DC8.36AC@igbmc.u-strasbg.fr> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) Hello everybody, DBWatcher Stabilised Version ========================================================================== I'm pleased to announce that version 2.00 of DBWatcher can be considered (at last...) as stabilised. Major bugs, which seriously limited the number of allowed searches per user, as well as minor bugs have been fixed. The new version is available from our anonymous ftp site : ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/ Hypertext Documentation ========================================================================== There now exists a documentation in HTML format which can be accessed at http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ or downloaded for local installation from ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/doc/ Mailing List ========================================================================== Until now, I have not been able to keep track of sites where DBWatcher has been installed. This would have been very useful though, not only for my personal records, but also to be able to provide a better support. I would be very grateful then if you could, please, let me know you have installed DBWatcher at your site by returning the completed little form below to plewniak@igbmc.u-strasbg.fr : 8<------------------------------------------------------------------------ Organisation : Contact person : e-mail address : Platform : OS : Do you run DBWatcher for local searches? Do you run DBWatcher for remote searches at NCBI? Do you use SetDBWatcher? Number of users (roughly) : Any comments? Any wishes? 8<------------------------------------------------------------------------ Thanks. I hope you'll find DBWatcher useful, Best regards to all, Fred Frédéric PLEWNIAK Bioinformatics I.G.B.M.C. Strasbourg - France From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!CRIS.COM!ketchup From: ketchup@CRIS.COM ("Ketchup") Newsgroups: bionet.software Subject: GeneDoc 2.0.1: Freeware Alignment Editor For Windows. Date: 4 Mar 1997 23:07:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 349 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703050708.CAA01806@newman.concentric.net> NNTP-Posting-Host: net.bio.net GeneDoc is freeware for MS/Windows. Please find more information at the web site. ---------------------- Greetings All, Please be informed that GeneDoc version 2.0.1 has been released to GeneDoc's web site: http://www.cris.com/~ketchup/genedoc.shtml Its been 6 months since the last release, and there has been plenty of work done. Lots of internal work on the program has been done so that there are no limitation or troubles on the amount of data that can be read or displayed. Screen routines are faster and printer routines work better. New printer options, Metafile support and much improved fasta and .msf file read routines. The toolbar and shading methods are much more flexible and intuitive to use. Two major biological features have been added. Secondary Structure shading and Super Family Group support. The Secondary Structure shading routines have been built on top of a generalized User Definable set of shading routines, so you can now use GeneDoc to shade sequences any way you can imagine. File Read routines for many of the Secondary Structure prediction output files created at EMBL are built in. GeneDoc reads DSSP files, also available at EMBL. Support for files from a new database of Secondary Structure information from PSC is provided. Use the User Defined routines to shade sequences with any prediction program. GeneDoc now provides support for organizing sequences in groups and do some nifty shading based on the groups. Apply structure information to each group, do group conserved, contrast and PCR contrast shading. I've included a more complete discussion of some of the new features in GeneDoc below. Sincerely, Karl Nicholas ketchup@cris.com ----- Written by Dr. Hugh Nicholas ------- Group and Structure Features of GeneDoc. Increasingly families of genes and proteins are organized into superfamilies. Database organizations often use a the percent of residue identity as the criterion for distinguishing whether a pair of sequences should be assigned to the same family or different families within a superfamily. Perhaps a more useful criterion is whether or not a gene duplication has taken place in the common evolutionary history of the two sequences. Evolutionary biologists use this classification and refer to homologous sequences that have only speciation events and not have gene duplication events in their common evolutionary history as being orthologous. Homologous sequences that have a gene duplication event in their common evolutionary history are referred to as paralogous. Orthologous genes or proteins generally carry out the same biochemical and physiological functions while paralogous proteins generally carry out similar but related functions. For instance, mammalian myoglobins, which carry oxygen within cells are a orthologous family. They are part of a superfamily that includes the alpha hemoglobins and the beta hemoglobins, both of which are also orthologous families. These three homologous families are part of the same paralogous superfamily, as are other globin genes and proteins. Families and superfamilies can be organized around functional criteria as well as evolutionary criteria and sequence divergence. Although all sixty plus transfer RNA sequences in E. coli are paralogous with each other they can be grouped together by their twenty amino acid acceptor activities. The group functions in GeneDoc are designed to allow users to work with and analyze groups based on any of the above criteria or any user determined criteria for dividing a set of sequences into groups. The first step in working with groups is to access the groups configuration dialog. The group configuration dialog can be accessed either by selecting the "edit sequence groups" item on the groups menu or by clicking the groups button, the button marked with an upper case G on the upper toolbar. The group configuration dialog allows the user to allocate the sequences to groups and to select a color to be associated with each group. For the purposes of most of the GeneDoc group analyses sequences that are not explicitly assigned to a group will be treated as if each unassigned sequence constitutes the only member of its own group. These implicit groups will not be analyzed but the sequences will be used in the analyses of the defined groups as "other" groups and thus they will contribute to the analysis. The group analyses result in different shading for individual groups. These shadings highlight different degrees of different kinds of conservation of residues or properties within and between groups. One analysis, referred to as the Dstat analysis, measures how different the groups are from one another and whether this difference is statistically significant. The Dstat analysis presents its results as a graph and numerical values. The simplest analysis is performed by the "shade group conserved" entry on the Groups menu. This analysis highlights positions within each group that are completely conserved, that is there is only one residue at that position within the group. This highlighting is done in the color assigned to the group in the group definition dialog. This measurement of conservation within the groups does not take into account any equivalency groups, even if they are active. The second thing this analysis does is to highlight the positions that are completely conserved across all of the groups, that is there is only one residue at that position for all of the sequences in the alignment. This part of the analysis does take the equivalency groups into account if they are in effect. The final action is to compute a consensus sequence based on the entire alignment. The most useful information derived from this analysis is to identify for the user the regions of the alignment where structural or functional requirements may have been relaxed or eliminated (or alternatively added as the group evolved a new function) for some groups relative to others. For this kind of information to be reliable the conserved groups need to be both large and from a diverse range of organisms. Otherwise the observed conservation may simply be the result of a small data set with highly dependent observations. A more stringent analysis is performed by the "shade group PCR contrast" entry on the Groups menu. Sites highlighted by this analysis meet two criteria. First is that a single residue is completely conserved within the group. Second this conserved residue does not appear, at that position, in any sequence outside of the group in which it is conserved. This analysis marks unique sequence features of the group that can be useful in defining a group motif and possibly in defining a primer sequence to be used in a polymerase chain reaction (PCR) amplification of the gene. The "shade group contrast" entry on the Groups menu performs an analysis similar to that of the "shade group PCR contrast" entry. This analysis makes use of the scoring table designated for alignment scoring to divide scores for pairs of amino acids into three classes, positive, negative, and neutral. The positive scores are those that are positive numbers in the similarity scores form of the table. Similarly, the negative scores are those that are negative numbers in the similarity scores form of the table, while the neutral scores have a zero score. The scores are stored in GeneDoc as distance or dissimilarity scores and hence must be converted to the similarity form. This is done by subtracting the score for a pair of sequence residues in the table from a constant called the zero cost distance, stored with the table. Thus the largest distances become negative similarities and small distances become positive similarities. The interpretation of the scoring tables is that positive similarities are conservative substitutions and are favored over random substitutions in the evolutionary process relating the sequences. The analysis performed by the "shade group contrast" entry on the Groups menu is less restrictive about the degree of conservation within the group than is . All of the sequence residues found at a position within the group are required to have a positive similarity score with each other, and thus to be conservative substitutions. This analysis is, however, more restrictive than is the analysis performed by the "shade group PCR contrast" entry on the Groups menu when dealing with residues outside the group. The residues outside of the group must have a negative similarity score with every residue from within the group, thus they are not allowed to be either conservative or neutral substitutions. An example of using this kind of analysis to study the recognition of transfer RNAs by aminoacyl tRNA synthetase enzyme can be found in McClain and Nicholas, 1987. Nicholas et al., 1987 describes using the contrasts to plan site directed mutagenesis experiments to confirm the analysis of the tRNAs. The analysis called the Dstat analysis is the Kolmogorov-Smirnov test for the equality of two distributions. The Dstat analysis is accomplished by first selecting a region (or all) of the alignment for use in the test calculations. Then you can either select the analysis under the Dstat menu or click the Dstat tool bar button. The Dstat toolbar button is near the right end of the upper toolbar and is marked by a pair of "S" shaped curves representing the cumulative distributions used in the test. As noted above, the Dstat analysis is a statistical test of whether the groups defined by the user are significantly different from each other. The first step in the test is to compute an alignment score for each pair of sequences over the region selected by the user. These scores are the partitioned into two distributions. The first distribution is composed entirely from scores where both of the sequences used to compute the score are members of different user defined groups. This is called the between groups distribution. The second distribution is composed entirely from scores where both of the sequences used to compute the score are members of the same user defined group. Note that this includes scores from every group with two or more sequences. This distribution is called the within groups distribution. These two distributions are plotted as cumulative distributions. That is the score is plotted versus the fraction of the scores in the distribution that are less than or equal to the score being plotted. The Kolmogorov-Smirnov D statistic (Dstat) is the maximum difference between the two distributions (along the fractional axis). Recent advances in the understanding of the distribution of values taken on by Dstat allow us to compute its one-sided significance probability. The one-sided significance probability is used rather than the two-sided significance probability because we are only interested in the case where the between groups distribution is composed of larger scores than the within groups distribution. The other situation, where the within groups distribution is composed of larger scores than the between groups distribution corresponds to either convergent evolution or some sort of selection in favor of divergence, situations that are not usually part of the hypothesis. The Kolmogorov-Smirnov test was selected instead of the more common Student's t test or the F test because it is sensitive to both the location of the distributions along the scores axis and to the shape of the distribution. Student's t test is sensitive to only the location of the distributions and the F test is sensitive only to differences in the variance of the distribution, only one of several aspects affecting the shape of the distributions. Thus the Kolmogorov-Smirnov test can find the distributions to be different when either Student's t test or the F test might have failed. Because of this it is necessary for the user to examine the plot carefully to determine the exact nature of the differences in the two distributions being tested. The user should exercise care that the biological hypothesis being examined should lead to the type of difference actually observed. Examples of testing biological hypotheses with sequence data and the Kolmogorov-Smirnov test can be found in Nicholas and Graves, 1983 and in Nicholas and McClain, 1995. The Nicholas and Graves paper contains an extended discussion of formulating Kolmogorov-Smirnov tests that correspond to different kinds of biological hypotheses. The structure groups and shading facility provide an extremely powerful and flexible set of tools for integrating sequence information with structural information. The facility is flexible enough to allow the user to display almost any kind of information as color codes along the sequence. Such states can include the obvious secondary structure state of the residue in the three dimensional structure. Less obvious properties like the solvent accessible surface area of the residue or its side chain can also be displayed. The fraction of the side chain in a polar environment is another characteristic that is sometime informative. One of the most powerful kinds of integration of structure and sequence information allows the user to visually examine the variation in structure or some structural property that occurs as the sequence varies in a series of homologous proteins. This same display allows the user to adjust the alignment based on information derived from the varying structures of a series of homologous proteins. Alternatively, you can have several copies of the same sequence in the alignment by adding additional copies with different names through the sequence import facility. Remember that each copy must have its own distinct name. These copies of the same sequence can all be highlighted using a different property. This allows you to easily visualize possible correlation of properties or of properties with sequence or structure. Another use for multiple copies of a single sequence in the alignment is to contrast predictions of structure and properties with that observed in an experimentally determined three dimensional structure. A wide spread use of the structure shading is to project the structure or properties from a sequence of known structure onto sequences whose structures have not be experimentally determined. This is accomplished by combining the structure shading facility with the group facility. At the same time you use the structure shading dialogue to associate a structure file with a specific sequence in the alignment you can designate that sequence as the master sequence of a structural group. This allows you to associate several sequences with a single structure file. These associated sequences will be shaded with the same colors in the same column of the alignment as the master sequence regardless of the sequence residue present in thhat position of the sequence. Thus this is essentially a low resolution homology modeling facility. All of these features can be combined into a very informative display for studying structure-function relationships in the following procedure. First, associate a structure file with each sequence in your alignment whose structure has been determined by X-ray crystallography or NMR. Make these sequences the master sequence for a group of the most closely related sequences in the alignment. Ideally the sequences within each group should have common biochemical properties such as substrate specificity, while different groups can have different substrate specificities. Use the sequence editing facility to put sequences in the same group on adjacent rows of the alignment. Put the group master sequence at the top of each group. Then set the display mode to differences mode and make sure this is applied to all of the groups. This yields a display with all of the group master sequences, that is the sequences with known structures, displayed with all of their residues. The other sequences in each group have a dot displayed where they have the same sequence residue as the group master. Sequence residues that are different from the group master sequence are shown. This highlights substitutions within each group that are presumably successful site directed mutagenesis experiments performed by nature. Differences between groups may be associated with the change in substrate specificity or other property. It can be very helpful to have exactly the same alignment in a second window highlighted in group contrast mode. This combination of displays can be a very powerful tool for examining structure-function relationships by integrating a large amount of information in an easy to comprehend format and presentation. Nicholas, H.B. Jr., and Graves, S.B. 1983. Clustering of transfer RNA by cell type and amino acid specificity. Journal of Molecular Biology, vol. 171, pp. 111 - 118. Nicholas, H.B., Jr., Chen, Y-M., and McClain, W.H. 1987. Comparisons of transfer RNA sequences. Computer Applications in the Biosciences, vol. 3, p. 53. McClain, W.H. and Nicholas, H.B,Jr. 1987. Discrimination between transfer RNA molecules. Journal of Molecular Biology, vol. 194, pp. 635 - 642. Nicholas, H.B. Jr. and McClain, W.H. 1987. An algorithm for discriminating transfer RNA sequences. Computer Applications in the Biosciences, 3, pp. 177 - 181. Nicholas, H.B. Jr. and McClain, W.H. 1995. Searching tRNA Sequences for Relatedness to Aminoacyl tRNA Synthetase Families. Journal of Molecular Evolution, vol. 40, pp. 482-486. From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!news.enteract.com!news.inetnebr.com!netserv.unmc.edu!news.mid.net!sunbird.usd.edu!news.uni.edu!news.physics.uiowa.edu!newsrelay.iastate.edu!news.iastate.edu!not-for-mail From: ckafer@iastate.edu (Chris Kafer) Newsgroups: bionet.software Subject: Blast client for windows?? Date: Sun, 02 Mar 1997 08:45:13 GMT Organization: Iowa State University, Ames, Iowa, USA Lines: 12 Message-ID: <33193cfe.177025013@news.iastate.edu> NNTP-Posting-Host: isum1.iastate.edu X-Newsreader: Forte Free Agent 1.1/32.230 I at one time had a Blast winsock client for windows that I used to send queries. Unfortunately, when my hard drive went up in smoke a while back, I lost it. I cannot seem to find the software on the 'net. Anybody know where it can be found? Thanks in advance! ************************************************************************ Chris Kafer www.public.iastate.edu/~ippm PGP Key available www.public.iastate.edu/~thorn ************************************************************************ From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!NANTES.INRA.FR!choiset From: choiset@NANTES.INRA.FR (CHOISET Yvan) Newsgroups: bionet.software Subject: drawing plasmid Date: 4 Mar 1997 22:10:44 -0800 Organization: INRA LEIMA Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <331D8E79.4FE3@nantes.inra.fr> Reply-To: choiset@nantes.inra.fr NNTP-Posting-Host: net.bio.net Hello I m looking for free software for drawing plasmid. Thanks for your help Yvan From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!ais.net!news.stealth.net!uunet!in2.uu.net!128.250.1.21!munnari.OZ.AU!harbinger.cc.monash.edu.au!newshost.carno.net.au!leonard.anu.edu.au!not-for-mail From: hxa228@leonard.anu.edu.au (Holger Averdunk) Newsgroups: bionet.software Subject: recombination-detection-program Date: 5 Mar 1997 13:53:25 +1100 Organization: Australian National University Lines: 3 Message-ID: <5fin75$k2k@leonard.anu.edu.au> NNTP-Posting-Host: 150.203.2.15 Keywords: recombination,gene conversion,sequence analysis X-Newsreader: NN version 6.5.0 #12 (NOV) Does anyone know of software which detects recombination/gene conversion in a set of (aligned) DNA/RNA/AA sequences ? Holger Averdunk holger@hercules.anu.edu.au From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!newsmaster From: Armel Le Bail Newsgroups: bionet.software Subject: Re: Software for 3-D graphics! Date: Wed, 05 Mar 1997 17:31:15 +0100 Organization: Laboratoire des Fluorures - Universite du Maine - France Lines: 14 Message-ID: <331D9FD3.128F@fluo.univ-lemans.fr> References: <5fdjkl$cmc$1@news.cc.umr.edu> Reply-To: armel@fluo.univ-lemans.fr NNTP-Posting-Host: pcb4122.univ-lemans.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Raghavender Pillutla wrote: > Can anyone tell me where I can find a software that can display simple > objects in 3-D? Specifically, I want to know if there is any programs > which can display spheres when I give the radius and the x,y,z > coordinates of the center. Pl. help. thanks in advance. VRML is not a bad solution. A list of softwares dedicated to crystallography, and much more, may be obtained at : http://fluo.univ-lemans.fr/vrml/intvrml.html Best wishes, Armel Le Bail From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Martin.Trick@bbsrc.ac.uk (Martin Trick) Newsgroups: bionet.software Subject: Output browser for Blast2 Date: 5 Mar 1997 15:25:52 GMT Organization: John Innes Centre Lines: 12 Message-ID: <5fk3a0$k92@is.bbsrc.ac.uk> NNTP-Posting-Host: pc0419.jic.bbsrc.ac.uk X-Newsreader: WinVN 0.92.1 I've recently got the Blast2 distribution and was very impressed. One small problem though is that the Blast Output Browser (BoB) that we routinely use here can't seem to handle the output files (I admit my tests weren't exhaustive). Maybe the btab program it uses isn't dealing with the gap characters that are now allowed in the alignments?? Does anybody know whether btab is (will be) updated or know of an alternative browser? Martin Trick (Martin.Trick@bbsrc.ac.uk) From owner-software@net.bio.net Tue Mar 04 22:00:00 1997 Newsgroups: bionet.software Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!europa.clark.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsxfer3.itd.umich.edu!portc01.blue.aol.com!newsstand.cit.cornell.edu!newstand.syr.edu!hood.cc.rochester.edu!troi.cc.rochester.edu!cjrm From: cjrm@troi.cc.rochester.edu (Christopher Jerome) Subject: Re: Software for 3-D graphics! Message-ID: <1997Mar3.193457.28638@galileo.cc.rochester.edu> Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: troi.cc.rochester.edu Organization: University of Rochester, Rochester NY References: <5fdjkl$cmc$1@news.cc.umr.edu> Date: Mon, 3 Mar 97 19:34:57 GMT Lines: 10 I believe that Corel Dream (with the Corel Draw 6 package) will let you define spheres by inputting parameters. Otherwise there are numerous cad software packages that will do so. You can download many through Ziff Sofware on compuserve and you may be able to find some 3-D graphics utils at www.shareware.com Chris Jerome cjrm@troi.cc.rochester.edu From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!news.maxwell.syr.edu!newsfeeds.sol.net!ix.netcom.com!news From: edwinl1@ix.netcom.com(MO & Associates) Newsgroups: bionet.software Subject: Sugestion Box/New Ideas Administrator Software Date: 6 Mar 1997 03:24:47 GMT Organization: Netcom Lines: 29 Message-ID: <5flddv$ntv@sjx-ixn8.ix.netcom.com> NNTP-Posting-Host: mia-fl6-17.ix.netcom.com X-NETCOM-Date: Wed Mar 05 7:24:47 PM PST 1997 THE NEW IDEAS ADMINISTRATOR Version 2.01 The best "NEW IDEAS ADMINISTRATOR" in the market. Use e-Mail (optional). Intuitive way for employees to have access to a tool in order to make suggestions to Supervisors. Can be done using computer or filling the new idea form. Can be e-mailed (optional) to his/her supervisor, director, vice-president, etc. The supervisor evaluates the idea and sends back the evaluation, asking for more info or with the final evaluation. Awards might be implemented depending the amount saved by the company. Also has different level of access, employee, supervisor, director, administrator, etc. Your Company can save millions. It can be customized for your needs. Also Help screens available. All kind of reports. Upgrades twice a year. Also help available through Internet. It's a simple but Powerful Tool for just: $139.99 Send Check or Money Order - $139.99 to: MO & Associates 666 W 81 St. 117 Hialeah, FL 33014 (The response has been so big that we need 4 to 8 weeks to process.) Satisfaction Guaranteed Ask for more info to: edwinL1@ix.netcom.com From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!HERCULES.SDSC.EDU!bourne From: bourne@HERCULES.SDSC.EDU (Philip Bourne) Newsgroups: bionet.software Subject: WPDB v2.2 Date: 5 Mar 1997 19:03:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Philip Bourne NNTP-Posting-Host: net.bio.net WPDB v2.2 Now Available http://www.sdsc.edu/pb/wpdb ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/ To subscribe to the mailing list: Send the message subscribe wpdb to majordomo@sdsc.edu J. App. Cryst. 1995, 28(6) 847-852. WPDB is a protein structure database search and display tool for use on Windows 3.1, Windows 95 and Windows NT platforms. WPDB is useful for detailed analysis of a single structure or comparative analysis of two or more structures. It comes with a variety of databases, including a 10-fold compressed version of the complete PDB downloadable via ftp. Alternatively, you can build your own database from PDB files with the WPDB Loader (WPDBL). Details can be found on the Web page indicated above. The major enhancement in v2.2 is a much improved 3-D structure viewer. WPDB is developed and maintained by Ilya Shindyalov and Phil Bourne at the San Diego Supercomputer Center. From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!europa.clark.net!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cliffs.rs.itd.umich.edu!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!newsmaster From: Armel Le Bail Newsgroups: bionet.software Subject: Re: Software for 3-D graphics! Date: Thu, 06 Mar 1997 12:03:15 +0100 Organization: Laboratoire des Fluorures - Universite du Maine - France Lines: 9 Message-ID: <331EA473.7450@fluo.univ-lemans.fr> References: <5fdjkl$cmc$1@news.cc.umr.edu> <331D9FD3.128F@fluo.univ-lemans.fr> Reply-To: armel@fluo.univ-lemans.fr NNTP-Posting-Host: pcb4122.univ-lemans.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Armel Le Bail wrote: > VRML is not a bad solution. A list of softwares dedicated to > crystallography, and much more, may be obtained at : Sorry, the URL was inexact, the true one is : http://fluo.univ-lemans.fr:8001/vrml/intvrml.html Armel Le Bail From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Alexey M. Eroshkin" Newsgroups: bionet.software Subject: Multiple sequence editor ProMSED2 is available thru IUBio archive Date: 6 Mar 1997 11:32:09 -0000 Organization: State Research Center of Virology and Biotechnology VECTOR Lines: 74 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fm9vp$q8f@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: bio-soft@dl.ac.uk Dear all, Multiple sequence editor ProMSED2 (Win) is available now thru IUBio archive as ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.exe and .readme --------------------------------------------------------------- ProMSED2: Protein Multiple Sequence EDitor-2 for Win 3.11/95 State Research Center of Virology an Biotechnology "Vector" Institute of Molecular Biology Koltsovo, Novosibirsk Region, 633159 Russia ProMSED2, Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. The program reads main sequence formats and performs automatic alignments, alignment visualization and editing and it allows sequences to be aligned interactively leaving unchanged previously aligned regions. The program has an user-friendly interface. Manual alignment and sequence analysis are facilitated by coloring schemes reflecting amino acid similarity in mutational, physico-chemical and other properties. Although ProMSED was targeted at protein sequences, it can be used on DNA sequences as well. The program provides flexible tool for sequences alignment, analysis, visualization, edition and presentation preparation. The program does or has (+ - NEW or enhanced features): + inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta), MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL formats; o has interface and functions like in others Windows applications (source file view, font changing, marking/unmarking, block and sequence selection, cut and paste, UNDO, etc.); o loads several sequence families in different windows, adds sequences to existing alignment, combines sequences from various files; + outputs the alignment in several popular formats; + makes presentation quality color and black-and-white prints of complete alignment or any selected block; + saves alignment picture as Windows metafile and bitmap; o permits to apply automatic alignment interactively (with options to change the alignment parameters) to any selected part of sequences of marked block; + calculates sequence similarity of complete sequences, of any selected sequence subset or of marked block in % and in PAM250 units (matrix of amino acid similarity); + calculates total (average for %) sequence similarity value - an estimation of alignment quality; + prints sequence similarity matrix; + sorts sequences by similarity of complete sequences or marked block; + displays conserved and semiconserved positions; + has many amino acid coloring schemes aimed to facilitate manual alignment and understanding protein sequence features. Some schemes are: EVOLUTIONARY CONSERVATIVE (reflects amino acid mutational properties), COMPLEX (similarity of amino acids in physico-chemical properties), HYDROPHOBICITY, CHARGE, BIG RESIDUES, ALPHA-HELIX, HELIX-BREAKERS, etc. The options to input user-defined schemes or change the colors of any amino acid groups are available; + searches subsequences and complex sequence patterns; o has complete HELP. Educational version is restricted in number and length of sequences. Comments, bug reports and suggestions for new features are welcome and should be sent by email to eroshkin@vector.nsk.su. We would be happy to get feedback from you. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Anatoly Frolov & Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.software Subject: ANNOUNCEMENT: FEBS advanced course: frontiers of protein structure prediction 1997 Date: 6 Mar 1997 09:23:56 -0000 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fm2fc$eh8@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: Call for applications =================================== FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.cam.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid) Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), B. Rost (Heidelberg) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.cam.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.software Subject: ANNOUNCEMENT: have you a protein to predict? Call for prediction targets Date: 6 Mar 1997 09:24:01 -0000 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fm2fh$eht@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: Call prediction targets ===================================== The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.cam.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.cam.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news.belwue.de!stremob.pci.chemie.uni-tuebingen.de!user From: kaifr@uni-tuebingen.de (Dr. Kai-Uwe Froehlich) Newsgroups: bionet.software Subject: Re: drawing plasmid Date: Thu, 06 Mar 1997 08:51:00 +0100 Organization: Phys.-chem. Institut, Universitaet Tuebingen Lines: 56 Distribution: world Message-ID: References: <331D8E79.4FE3@nantes.inra.fr> NNTP-Posting-Host: stremob.pci.chemie.uni-tuebingen.de In article <331D8E79.4FE3@nantes.inra.fr>, choiset@nantes.inra.fr wrote: > Hello > > > I m looking for free software for drawing plasmid. > > Thanks for your help > > Yvan Hi Yvan, You do not specify the platform (computer type) you need the program for. If it is for a Macintosh, you should have a look at a plasmid drawing program I have written, primarily for our lab use (so it is anything but polished), which I have released as Freeware. It converts lists of restriction sites and fragment/gene positions into Postscript files. Its weak points in short - It is a Hypercard stack, so you need Hypercard to run it (luckily, speed is no problem, there are no processor intensive steps involved) - The output are Postscript files in Illustrator format. To view and to further edit the picture (which you will have to, see below), you need either Adobe Illustrator, or the Shareware EPStoPICT, which produces a fully editable, object oriented PICT version of the graphics. - The program does not care for overlapping labels, so in most cases you must do some fine-tuning On the other hand, the program - allows "electronic cloning", so you can quickly construct new plasmids from those already entered in the program - can draw all plasmids at the same size, but also using the same (or any you want) scale (that was the primary reason for me to write the program, most commercial programs had (still have?) no way to specify the drawing scale (except by different magnification in the page setup) - draws linear and circular maps, allows borders of various widths and fills of grays, arrows... - output quality is great, thanks to Postscript - the price is right :-) For a more detailed description, including screen shots of the output graphics, see and that is also the place to download the stack: (BTW, there is also a stack for the organization of plasmid/strain collections available) Kai ----------------------------------------------------------------------- Dr. Kai-Uwe Froehlich, Physiologisch-chemisches Institut, Hoppe-Seyler-Str. 4, 76072 Tuebingen, Germany From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!EU.net!news2.EUnet.fr!vodka.cephb.fr!not-for-mail From: Mourad Sahbatou Newsgroups: bionet.general,bionet.genome.chromosomes,bionet.molbio.gene-linkage,bionet.software Subject: THE CEPH GENOTYPE DATABASE V8.1 AVAILABLE Date: Thu, 06 Mar 1997 17:53:47 +0100 Organization: Fondation J. DAUSSET - C. E. P. H. Lines: 33 Message-ID: <331EF69B.4ED0@cephb.fr> NNTP-Posting-Host: vodka.cephb.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 5.4 sun4d) CC: mourad.sahbatou@cephb.fr Xref: biosci bionet.general:25916 bionet.genome.chromosomes:1553 bionet.molbio.gene-linkage:1344 bionet.software:18066 THE CEPH GENOTYPE DATABASE V8.1 AVAILABLE ON WEB AND FTP SERVERS. The most recent version of The CEPH genotype database (V8.1) is now available to the scientific international community. The database holds over 2,530,000 CEPH family genotypes generated during the last 13 years for some 11,932 polymorphic markers, including more than 8,900 microsatellite markers ( 57% of which are hightly polymorphic). The mean heterozygote frequency of the loci in V8.1 is 0.64, and the mean number of alleles per locus is 6.2, essentially reflecting the large number of microsatellites in the database. In addition to the raw genotypes, the database provides users with linkage file formats of markers and two-point lod scores among all pairs of markers on the same chromosome (3,544,000 two-point lodscores have been computed). You can efficiently browse and dump the data from our Web/database interface (http://www.cephb.fr/cephdb/). Dump programs allow you to dump data for several markers on the same chromosome in CEPH, LINKAGE and CRIMAP formats. CEPH anonymous FTP server : ftp://ftp.cephb.fr/pub/ceph_genotype_db/ CEPH genotype database Web server : http://www.cephb.fr/cephdb/ CEPH World Wide Web home page : http://www.cephb.fr CEPH database manager : cephdbm@cephb.fr ---------------------------------------------------------------------- Mourad SAHBATOU Fondation Jean DAUSSET - CEPH CEPH database manager 27, rue Juliette Dodu cephdbm@cephb.fr 75010 Paris, France From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Newsgroups: bionet.info-theory,bionet.software Path: biosci!rutgers.rutgers.edu!news.sgi.com!newsfeed.nacamar.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: Ask for materials on bioinformatics Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Date: Thu, 6 Mar 1997 14:19:58 GMT To: fuellen References: <9703050520.AA20572@beloit.edu> Nntp-Posting-Host: salbei.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 44 Xref: biosci bionet.info-theory:4976 bionet.software:18065 Zhang Ren wrote, >Hi, Dear friends: > >I am very interested in Bioinformatics. Can anyone provide me some >materials on some introductory courses on Bioinformatics or some >papers ( or web sites) containing that topic? You may wish to take a look at the material assembled for the VSNS-BCD BioComputing Course, at http://www.techfak.uni-bielefeld.de/bcd/welcome.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/welcome.html http://www.biotech.ist.unige.it/bcd/welcome.html In particular, we currently need feedback on our new addition, ``Biocomputing For Everyone'', at http://www.techfak.uni-bielefeld.de/bcd/ForAll/welcome.html I'm glad to receive any comments, questions, praise and criticism :) Also, does anyone know a popular science mag which may be interested in this material ? Thanks to all contributors (most of them have submitted a self-description at http://www.techfak.uni-bielefeld.de/bcd/Faculty/members.html), and to David Steffen/MCBR and Paolo Romano/ABC Genoa for providing the mirrors. best wishes, Georg Fuellen, fuellen@dali.mathematik.uni-bielefeld.de, fuellen@ alum.mit.edu Univ. Bielefeld, Research Group in Practical Comp. Science, Fax +49 521 106 6411 Http://WWW.TECHFAK.UNI-BIELEFELD.DE/techfak/persons/fuellen/ , Fon .... 106 2903 >Thank you in advance! > >My address: > >Dr. Zhang Ren >c/o Dr. Chun-Ting Zhang >Department of Physics >Tianjin University >Tianjin 300072 >China > >or e-mail me at: ctzhang@tju.edu.cn > >Zhang Ren From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!news-paris.gsl.net!news.gsl.net!rain.fr!jussieu.fr!univ-lyon1.fr!news.imag.fr!grenet.fr!usenet From: hewat@ill.fr (Alan Hewat) Newsgroups: bionet.software Subject: Re: Software for 3-D graphics! Date: 6 Mar 1997 15:21:38 GMT Organization: ILL Grenoble France (High Flux European Research Reactor) Lines: 25 Sender: -Not-Authenticated-[3178] Message-ID: <5fmne2$2m3@naiad.grenet.fr> References: <5fdjkl$cmc$1@news.cc.umr.edu> NNTP-Posting-Host: firewall.esrf.fr X-Newsreader: InterNews 2.0.1@machew.ill.fr[U] XDisclaimer: User not authenticated Raghavender Pillutla writes: > Can anyone tell me where I can find a software that can display simple > objects in 3-D? Specifically, I want to know if there is any programs > which can display spheres when I give the radius and the x,y,z > coordinates of the center. Make a file like this and get VRweb from: http://www.iicm.edu/vrweb for almost any machine Unix, PC etc #VRML V1.0 ascii Separator { #start object Material { diffuseColor 1 0 0 #red body specularColor 1 1 1 #white hilights shininess 0.1 } #shiny Sphere { radius 1.5 } #draw sphere Translation { translation 2 0 0 } #translate Material { diffuseColor 0 1 0 } #green body Sphere { radius 2.5 } #draw sphere } #finish object Look at http://www.ill.fr/dif/3D_crystals.html for further details. Alan Hewat, ILL Grenoble, FRANCE (hewat@ill.fr) fax (33) 76.48.39.06 ftp://ftp.ill.fr/pub/dif http://www.ill.fr/dif/ From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!fido.news.demon.net!demon!news.unisource.nl!xs4all!not-for-mail From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: SeqSearch v1.1 for Windows Date: 6 Mar 1997 07:07:34 GMT Organization: XS4ALL, networking for the masses Message-ID: <5flqfm$ild$1@news1.xs4all.nl> NNTP-Posting-Host: asd17-25.dial.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Thu, 06 Mar 1997 08:07:34 CET X-Newsreader: WinVN 0.99.7 Lines: 19 SeqSearch v1.1 for Windows is now available. It is a DNA analyis package for the daily routines in a molecular biology lab. It offers the following features: - multi user/project database - seperate databases for sequences,plasmids,contructs,oligo's and motifs - extended restriction site analysis with -user defined- enzym sets - clone bench for designing constructs - silent mutagenesis analysis - codon mutation primer design - mismatch primer design - fragment mapping with gel simulation - motif search - protein hydrophobicity plots - reading frame analysis A evaluation version can be found at http://www.xs4all.nl/~marker From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.software Subject: ANNOUNCEMENT2: have you a protein to predict? Call for prediction targets Date: 6 Mar 1997 12:35:03 -0000 Lines: 39 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fmdln$232@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk [sorry - with correct web addresses this time] Announcement: Call prediction targets ===================================== The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news.niehs.nih.gov!not-for-mail From: Nick Staffa Newsgroups: bionet.software Subject: Animal randomization program? Date: Thu, 06 Mar 1997 16:20:57 -0500 Organization: NIEHS Lines: 13 Message-ID: <331F3535.1ED2@niehs.nih.gov> NNTP-Posting-Host: mickeyfinn.niehs.nih.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) I am interested in acquiring a program for animal randomization, preferably for windows 95. Program should divide animals into weight classes and dose groups and randomly assign them to cages --- a thing that I believe is done often in animal studies. Any information would be welcome. Thank you Nickolas G. Staffa, Jr. National Institute of Environmental Health Sciences Research Triangle Park, NC 27709 staffa@niehs.nih.gov From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!newsfeed.uk.ibm.net!ibm.net!newsfeed.de.ibm.net!ibm.net!02-newsfeed.univie.ac.at!01-newsfeed.univie.ac.at!swidir.switch.ch!swsbe6.switch.ch!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.software Subject: Free molbio prg available here ! Date: Thu, 06 Mar 1997 18:20:12 +0100 Organization: Univerity of Zurich Lines: 46 Message-ID: <331EFCCB.33EE@vetvir.unizh.ch> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: 130.60.22.38 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Hi there I am presently looking for molecular biologists willing to test some programs I made aimed speeding up the daily lab work ! - This is how it works: The programs are accessible over the WWW, no downloading is required, all you have to do is download a free plugin program to enhance the browser you are using (Netscape 2.x and Internet Explorer 2.x only) on your Mac or Windows computer ! - What you have to do first: Download the appropriate plugin program and install it on your computer, here is the URL: http://www.unizh.ch/vetvir/plugin.html - Then connect to: http://www.unizh.ch/vetvir/programs.html These are the programs which make your live as a molecular biologist easier ! a. Digest Preview : this program allows you to run a virtual agarose gel based on the nt sequence of the DNA you are cutting with appropriate restriction enzymes. You will see the expected (calculated) bands on the virtual agarose gel before you go to the UV box to take a picture. b. Dilution Calculator which does all the work to dilute does x.xM solutions standing around to the one you need. (Can‘t follow) c. Adaptor Design: creates an adapter for ligation of an insert which has no compatible ends. All programs are in development stage. I like to get your feedback ! Specially from people which use Windows computers ! Regards Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!howland.erols.net!worldnet.att.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.ums.edu!news.ab.umd.edu!not-for-mail From: dbradbur@umabnet.ab.umd.edu Newsgroups: bionet.software Subject: dna sequence analysis software Date: Thu, 06 Mar 1997 22:10:12 GMT Organization: University of Maryland at Baltimore Lines: 7 Message-ID: <5fnf51$5j8$1@raven.ab.umd.edu> NNTP-Posting-Host: cfs12.ab.umd.edu X-Newsreader: Forte Free Agent 1.0.82 Anyone know of a program that can read DNA sequence off a scanned image of a DNA sequence film? Thanks, David L. Bradbury dbradbur@umabnet.ab.umd.edu From owner-software@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.software Subject: ANNOUNCEMENT2: FEBS advanced course: frontiers of protein structure prediction 1997 Date: 6 Mar 1997 12:35:17 -0000 Lines: 75 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fmdm5$23l@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk [sorry - with correct web addresses this time] Announcement: Call for applications =================================== FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid) Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), B. Rost (Heidelberg) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-software@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-lyon1.fr!news From: bioch@lnsd-res.univ-lyon1.fr (biochimie) Newsgroups: bionet.software Subject: Re: Looking for digital image analysis software Date: 7 Mar 1997 10:31:08 GMT Organization: INSERM U189 Lines: 56 Message-ID: <5foqpc$lfo@tempo.univ-lyon1.fr> References: <5f9ubd$rca@dfw-ixnews12.ix.netcom.com> <5fevbl$1pt@taurus.fccc.edu> NNTP-Posting-Host: pc-bioch2.univ-lyon1.fr Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 In article <5fevbl$1pt@taurus.fccc.edu>, sauder@castor.fccc.edu says... > >In article aisoai@agc.co.jp (ISOAI Atsushi) writes: >>In article <5f9ubd$rca@dfw-ixnews12.ix.netcom.com>, kschap@ix.netcom.com >>(Kane L. Schaphorst) wrote: >> >>..... >> >>> While I believe these imaging systems may be adequate for figure >>> composition and image archival, I am not certain about this. Furthermore, >>> I do not know of any decent freely available or commercially available >>> software that can perform quantitative analysis on these images. To date, >>> the only image analysis >>>needed to perform is densitometry by either profile or volume analysis. >> >>Hi, >>I can not recommend the best imaging systems for your purpose, >>but if you have PC and scanner why not you try NIHImage. >>It's free but (I think) it's one of the best image software in >>the world. You can get it from: >>URL: http://rsb.info.nih.gov/nih-image/ >>Please try it. I hope it is useful for you. >>Atsushi Isoai, Ph.D. > > NIH-Image runs on the Mac. There was a beta version of a port >to the PC called Scion Image, I think. There's also a program called >ImageTool. Check out these URLs: > http://ddsdx.uthscsa.edu/dig/itdesc.html > http://rsb.info.nih.gov/nih-image/default.html > > Both these programs can do densitometry. >-- About The PC version of NIH Image: It's a Alpha version and we can't seriously rely on it (bugs !). You CAN'T do quantitative densitometry on proteins or DNA patterns with ImageTool ! May be you can use the following solutions : 1)A (very) good tabletop scanner (notice that the BioRad GS700 is no more than an AGFA ARCUS II) 2)A Image analysis software. I'm testing some of them: 1D-SCAN from Scanalytics (http://www.cspi.com/scanalytics/index.htm) SIGMAL-GEL from Jandel (http://www.jandel.com/) ImagePro Plus from Media Cybernectics (http://www.mediacy.com/mediahm.htm) I know that Bioscan offers this kind of solutions (http://www.bioscan.com/index.shtml) -- P.GEORGE (george@lnsd-res.univ-lyon1.fr) INSERM U189 LYON-SUD medecine school BP 12 69921 OULLINS CEDEX FRANCE Tel :33-4-78-86-31-58 Fax :33-4-78-50-71-52 From owner-software@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!metro.atlanta.com!uunet!in1.uu.net!208.200.248.2!news.olypen.com!news From: gjw@olypen.com (Gordon Wanner) Newsgroups: bionet.software Subject: Quick Deposit for Windows, Merchant Credit Card Software Date: 6 Mar 1997 21:00:56 GMT Organization: Olympic Software Publishing Co. Lines: 10 Message-ID: <5fnba8$8bj@news.olypen.com> NNTP-Posting-Host: annex-t1-9.olypen.com Mime-Version: 1.0 X-Newsreader: WinVN 0.99.4 If you are sick and tired of dropping to DOS to authorize your customers credit cards, or ending up with unusable data… It's time to switch to Quick Deposit for Windows™. This easy to use software is designed for mail order and retail merchants! Quick Deposit works under Win3.XX, Win95 and NT. Completely Certified by First Data Corp. (CES) Quick Deposit also takes advantage of magnetic card swipe equipment and incorporates the latest address verification technology CPS 2000. Quick Deposit for Windows™. creates OLE 2.0 compatible data, which can be used with most other Windows Applications. For a fully functional free trial version visit www.olypen.com/gjw/qd.htm From owner-software@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!hammer.uoregon.edu!arclight.uoregon.edu!newsfeed.direct.ca!newsgate.direct.ca!usenet From: pnorrish@direct.ca (Paul Norrish) Newsgroups: bionet.software Subject: Do you need a handy little address book and phone dialer for windows Date: 7 Mar 1997 16:10:46 GMT Organization: PM Enterprises Lines: 10 Message-ID: <5fpem6$i3e$1@orb.direct.ca> NNTP-Posting-Host: van-as-10c16.direct.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 I wrote an addess book and phone dialer for windows,its really good and simple.you can download the demo off my homepage at " http://mypage.direct.ca/p/pnorrish/ " or at " http://www.axxis.com/altus/products.html " It's called "my litle address book " by PM Enterprises Paul Norrish pnorrish@direct.ca From owner-software@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!news.maxwell.syr.edu!dispatch.news.demon.net!demon!troopers.demon.co.uk!troopers.demon.co.uk!dyoungmdl2 From: "Douglas J. Young" Newsgroups: bionet.software Subject: do you need any graphics created? Date: Fri, 7 Mar 1997 14:54:20 +0000 Organization: DYOUNGMDL2 Distribution: world Message-ID: References: <33193cfe.177025013@news.iastate.edu> NNTP-Posting-Host: troopers.demon.co.uk X-NNTP-Posting-Host: troopers.demon.co.uk MIME-Versi