From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!in2p3.fr!univ-lyon1.fr!pasteur.fr!oleane!not-for-mail From: "News Ikosoft" Newsgroups: bionet.software Subject: Image application quality Date: Wed, 2 Jul 1997 10:59:21 +0200 Organization: Guest of OLEANE - PIPEX International Lines: 27 Message-ID: <5pd4ts$gas$1@Helene.OLEANE.NET> NNTP-Posting-Host: dyn-2.mrs.oleane.com X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 We are a software company, developping image application for hairstyle industry. We have developped an application, MORGANE, enabling to try several haircut. Facing several difficulties we had finish with a readytosale product. But we are still looking for improving our image quality. So we will be please if you can check the freeware www.beautyplanet.com/ikosoft/morgane/morgane.exe in order to get your feedback. Thank you. Sincerely Yours. From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Alexey M. Eroshkin" Newsgroups: bionet.software Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/de sign Date: 2 Jul 1997 09:41:39 +0100 Organization: State Research Center of Virology and Biotechnology VECTOR Lines: 364 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5pd483$nlm@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: bio-software@dl.ac.uk To: bio-software@dl.ac.uk From: Alexey Eroshkin Cc: mutatiomn@net.bio.net, pop-bio@net.bio.net, peptides@dl.ac.uk, molmodel@dl.ac.uk, mol-evol@dl.ac.uk, microbio@dl.ac.uk, immuno@dl.ac.uk, hiv-biol@dl.ac.uk, fluorpro@dl.ac.uk, biophys@dl.ac.uk, bio-matrix@dl.ac.uk, proteins@dl.ac.uk, virology@dl.ac.uk, xtal-log@dl.ac.uk Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/design Dear all, new version of ProAnWin (Protein Analyst for Win 3.11/95) now publicly available from IUBio as ftp://iubio.bio.indiana.edu/molbio/ibmpc/paw.exe (and paw.readme) If you have access to e-mail only, the program can be obtained via e-mail by sending the following message: To: BITFTP@pucc.Princeton.EDU From: YOUR E-MAIL ADDRESS ftp iubio.bio.indiana.edu uuencode user anonymous cd molbio/ibmpc get paw.exe get paw.readme quit Server will return you UUENCODED program in several files. Running UUDECODE you'll get the archive with the program. ************************************** ProAnWin - Protein Analyst for Windows ************************************** version 3.01 Multiple sequence alignment, analysis of protein sequences and structures, structure-activity relationships, design of protein-engineering experiments Copyright(c)1995-97 I.Pika, A.Frolov, V.Ivanisenko, A.Eroshkin All Trademarks and Registered Names are acknowledged in this document. The files required to run ProAnWin are distributed in the form of a single compressed file (self-extracted). Create a directory "PROANWIN" on your hard disk, for example, C and copy the compressed file to the directory. Unpack the program (type PAW in DOS prompt and answer Yes to all questions). Once you extracted archive files, start Windows and start the program. This program is provided "AS IS" without any warranty, expressed or implied to you or any other person. The authors will not be liable for incidental, consequential or other damages arising through the use of this software. As the program is under further development the documentation may not reflect all current program options. PROGRAM CONTENT: Directory: Main directory - program modules DATA - files with amino acid physico-chemical properties, manual, examples with input and output files ALIGNS - aligned sequences of 50 protein families MAIN PROGRAM FEATURES (* - new feature) - Makes multiple sequence alignment - automatic (Clustal V) and manual, global and local (in selected region); - Threads multiple alignment onto known 3-dimensional structure; - Imports data in all major formats (SWISS-PROT, PIR, FASTA, GCG, Clustal); - Imports protein 3D structure from Protein Data Bank files (PDB format) - Inputs data on protein activities/property or phenotype; - Transforms activity values (log (A), ln (A), A/K, A+k, etc.); * Searches linear and spatial sites, conservative and variable in changes of specified physico-chemical properties (for example, helical hydrophobic moment); * Searches linear and spatial sites, having high and low values of specified physico-chemical properties (for example, Kyte-Doolittle hydrophobicity); * Plots sets of different physico-chemical profiles for individual protein sequence; * Plots specified physico-chemical profiles for the set of sequences; - Searches linear sites in multiple protein alignment and spatial sites in protein 3D structure influencing protein activity/property; * Plots average physico-chemical profile for the family of sequences; * Plots profile of dispersion of physico-chemical profiles for the family of sequences; * Plots physico-chemical profiles for protein 3D structure; - Analyses relationships between site structural characteristics and protein activities by multiple linear regression analysis; - Analyses structural differences between proteins divided by functional, evolutionary or other criteria; - Investigates physico-chemical factors related with activity changes in a set of mutant proteins; * Simulates protein-engineering experiments and predicts protein activity. Has options for automatic mutant generation (to increase or decrease protein activity) and for manual mutant generation; * Predicts activity for newly sequenced proteins; - Makes protein 3D pictures (mono and stereo) with sites highlighted; * Has more then 400 amino acid physico-chemical properties; - Investigates ten types of protein site characteristics, including average values, helical moments, beta-strand moments, etc.; - Saves results to the disk and saves pictures to the clipboard; - Has help and manual. ProAnWin PERMITS TO OBTAIN NEW RESULTS IMPORTANT IN BIOCHEMISTRY, MOLECULAR BIOLOGY ETC., AND TO DESIGN PROTEIN ENGINEERING EXPERIMENTS: 1. The program helps to find information that can not be found by other programs (activity/property-modulating sites, phenotype defining regions); 2. The user has an opportunity to conduct the analysis of structure-activity relationships in sequences and 3D structure. 3. The program permits to generate and to check up a plenty of hypothesis about the role of different sites and their various physico-chemical characteristics in protein activity, that is rather difficult or impossible at the "hand-operated" analysis. 4. Search of structure - activity relations is carried out with the use of multiple regression analysis and the results have statistical evaluations on reliability. 5. The user has an opportunity to work simultaneously with sequences and 3D protein structure (sites marked on the sequence are visualized in 3D structure and vise versa). 6. Alongside with the conventional average physico-chemical characteristics of a sequence site the user analyzes 9 additional characteristics of sequential (linear) sites and 5 characteristics of spatial sites. 7. The program permits considerably to reduce time during creation a mutant proteins with desired property. HOW TO START To investigate protein/peptide family of your interest you should have or prepare sequence data file(s). You can use alternatively sequences data files in FASTA (PEARSON), PIR, SWISS-PROT, CLUSTAL, GCG formats or in INTERNAL 1 format (3 data files with protein names (*.seq), protein activities or grouping (*.act) and aligned sequences (*.ali), see the examples in DATA directory) in the current directory. 3D protein structure you can take from PDB database. To use the program follow the steps: - start the program; - select sequences of the family you are going to investigate; - select a file with required physico-chemical properties of amino acids; - load protein 3D structure (if available); - define an investigated fragment (or up to 8 fragments); - define factors for analysis; and so on. All other information you'll get from MANUAL.TXT or HELP. ProAnWin IS USEFUL IN: - protein structure-function and structure-activity investigations; - designing proteins and peptides with improved activity; - making multiple protein alignments and getting sense from it; - studying phenotype-genotype correlations; - preparation of protein 3D pictures with sites highlighted; - protein features analysis; - comparative protein sequence analysis. PUBLICATIONS: 1. Frolov A.S., Pika I.S., Eroshkin A.M. ProMSED: Protein multiple sequence editor for Windows 3.11/95. CABIOS, 1997, 13, 243-248 2. Morozov B.M., Ivanisenko V.A., Eroshkin A. M., Ugarova N.N. Computer analysis of relations between bioluminescence color and primary structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), 1996, 30, 1167-1172. 3. Ivanisenko V.A., Pika I.S., Pinin S.I., Fomina T.I., Eroshkin A.M. Studying structure-activity and phenotype-genotype relationships in protein families. Methods, algorithms and applications. Folding and Design, 1996, 1, Suppl., p.84. 4. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin Y.V. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. CABIOS, 1995, 11, 39-44. 5. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program PROANAL for analysis of relationship between structure and activity in a family of proteins or peptides. CABIOS, 1993, 9, 491-497. 6. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev A.A. Analysis of peptide fragment insertions into major coat protein of bacteriophages M13, f1 and fd. Relation of protein structural characteristics and viability of mutant phages. Molec. Biology (Russia), 1993, 27, 1345-1355. The version installed has limit in the number of analyzed sequences (15). To get unlimited registered version please contact the authors. If you have problems running ProAnWin please consult the manual and HELP carefully to see if they can help. If you still need advice then please contact the authors by e-mail: eroshkin@vector.nsk.su or State Research Center of Virology an Biotechnology "Vector" Koltsovo, Novosibirsk Region, 633159 Russia Tel: (3832) - 647774 Fax: (3832) - 328831 Ask authors for the updated ProAnWin version and ADDITIONAL NEW SOFTWARE TOOLS ProMSED2, ProAnalyst: ProMSED2 ProMSED2, MS Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. ProMSED2 is the enhancement of ProMSED made according to user's remarks and suggestions. 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 presentations. Availability: EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.exe and .readme 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. ProAnalyst ProAnayst: DOS version of ProAnWin with additional functionality (single and multiple sequences analysis, profiles analysis, combinatorial libraries; design of protein engineering experiments) Availability: IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/panalys1 EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst Functions: o data conversion from several protein sequence formats (FASTA, SWISS-PROT, PIR, CLUSTAL). o databases with more then 50 amino acid physico-chemical properties; o inputs 3D protein structure in PDB format; o flexible VISUALIZATION OF PROTEIN 3d STRUCTURES with sites highlighted; o inputs user-defined protein activities, properties or related phenotypes; o searching SITES INFLUENCING PROTEIN ACTIVITY and analyzing relationships between protein site structural characteristics and protein activities (properties or related phenotypes); o multiple linear regression analysis of STRUCTURE-ACTIVITY relationships, discriminant analysis and ANOVA; o intra and cross group VARIABILITY analysis; o GENOTYPE -- PHENOTYPE CORRELATION analysis (e.g., for drug resistance in viruses); o alphabetical and physico-chemical analysis of protein features variations (in 1D and 3D structures); o structure-activity determination profile (SAD); o investigation of physico-chemical factors related with activity or property changes in MUTANT PROTEINS; o searching motifs in COMBINATORIAL LIBRARIES (peptide, phage- display libraries, etc.) with MOTIF MAPPING on the target protein; o design PROTEIN-ENGINEERING experiments; o ACTIVITY, PROPERTY AND PHENOTYPE PREDICTION; o sorting sequences by protein activity value, by protein group number and by number of motifs found; o mapping results on 3D structure and sequences. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. 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 Tue Jul 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!158.43.192.17!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!not-for-mail From: "News Ikosoft" Newsgroups: bionet.software Subject: image application quality. Date: Wed, 2 Jul 1997 10:53:27 +0200 Organization: Guest of OLEANE - PIPEX International Lines: 19 Message-ID: <5pd4iq$g3k$1@Helene.OLEANE.NET> NNTP-Posting-Host: dyn-2.mrs.oleane.com X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Dear sirs, We are developping image application related to hairstyles. We are always looking for an higher image quality. So, we will be please to get from you your feeedback about our MORGANE software. it is dowloadable at www.beautyplanet.com/ikosoft/morgane/morgane.exe . Thank you for your interest and your comments. Sincerely yours. From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!News1.Vancouver.iSTAR.net!news.istar.net!hammer.uoregon.edu!leto.ou.edu!news.ou.edu!news.ecn.uoknor.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: Chromas 1.42 Date: Mon, 30 Jun 1997 14:38:37 +0900 Organization: Griffith University Lines: 17 Message-ID: <33B7465D.5E74@nospam.see.below> NNTP-Posting-Host: gelpro.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Hi, Chromas 1.42 is now available on: http://trishul.sci.gu.edu.au/~conor/chromas.html I have fixed a bug which caused garbage characters to be displayed in the sequence for some files. The X-axis zoom can be adjusted on the printout, too. For those who don't know, Chromas is an ABI and SCF chromatogram viewer/basecall editor for Windows. Cheers, Conor The rest of my email address is sct.gu.edu.au. The first bit is in the 'From:' line above. From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gsl.net!news.gsl.net!hammer.uoregon.edu!leto.ou.edu!news.ou.edu!news.ecn.uoknor.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: Chromas 1.42 Date: Tue, 01 Jul 1997 10:25:03 +0900 Organization: Griffith University Lines: 17 Message-ID: <33B85C6F.6D31@nospam.see.below> Reply-To: c.mccarthy@nospam.see.below NNTP-Posting-Host: gelpro.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Hi, Chromas is an ABI and SCF chromatogram viewer/basecall editor for Windows. Version 1.42 is now available from: http://trishul.sci.gu.edu.au/~conor/chromas.html I have fixed a bug in the Windows 3.1 version which caused garbage characters to be displayed in the sequence of some files. Also, you can now set the X-axis zoom for the printout. Cheers, Conor The rest of my e-mail address is sct.gu.edu.au. The first bit is in the "From:" line above. From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!pravda.ucr.edu!news.cs.ucr.edu!zdc!super.zippo.com!newsfeed.direct.ca!news.maxwell.syr.edu!news.pangea.ca!news.mira.net.au!news.netspace.net.au!news.mel.connect.com.au!munnari.OZ.AU!bunyip.cc.uq.edu.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: Chromas 1.42 Date: Wed, 02 Jul 1997 21:49:46 +1000 Organization: Griffith University Lines: 16 Message-ID: <33BA405A.CC8@nospam.see.below> NNTP-Posting-Host: cornea.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) Hi, Chromas is a freeware Windows chromatogram viewer/basecall editor for ABI and SCF files. You can download it from: http://trishul.sci.gu.edu.au/~conor/chromas.html I have fixed a bug in the Windows 3.1 version which caused garbage characters to be displayed in the sequence of a few ABI files. Also, you can now set the X-axis zoom for the printout. Cheers, Conor The rest of my e-mail address is sct.gu.edu.au From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!dispatch.news.demon.net!demon!ffaltd.demon.co.uk!ffaltd.demon.co.uk!support From: Tech Support Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: Wed, 2 Jul 1997 15:13:05 +0100 Organization: Foster Findlay Associates Ltd Distribution: world Message-ID: References: <339BE6EB.2C7B@radium.uio.no> <5p8t6b$lc7$1@msunews.cl.msu.edu> Reply-To: Tech Support NNTP-Posting-Host: ffaltd.demon.co.uk X-NNTP-Posting-Host: ffaltd.demon.co.uk [158.152.30.179] MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.01 Lines: 23 >>I am also interested in image processing software. I need a program that >>can measure the area of several objects on the screen, and then sum up those >>areas and put the total on a single line in a data file. The objects would >>range from the size of pencil eraser to the size of a computer mouse. >>Terry M. Trier >>Entomology Department >>Michigan State University PC_Image does this. Look at the web site for more information and demo software to download. http://www.demon.co.uk/ffaltd/ Best regards, Dominique Miller. Foster Findlay Associates, * WWW: http://www.demon.co.uk/ffaltd/ Newcastle Technopole, TEL : 0191 201 2180 Kings Manor, FAX : 0191 201 2190 Newcastle Upon Tyne, * International: NE1 6PA TEL : ++ 44191 201 2180 ENGLAND. FAX : ++ 44191 201 2190 From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!panix!howland.erols.net!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!not-for-mail From: "Chuck Nelson" Newsgroups: bionet.software Subject: Chat with a Tech, Free... Date: 1 Jul 1997 18:18:49 GMT Organization: Free Tech Lines: 6 Message-ID: <01bc8612$2a7b7ac0$4618adcf@chuck> NNTP-Posting-Host: pm3-5.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 Want to ask a tech, a question? PC software, hardware questions.. Free Technical Support. Come to: http://www.free-tech.com From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!not-for-mail From: Frederic PLEWNIAK Newsgroups: bionet.software,bionet.software.gcg Subject: Re: Exon Mapping Date: Wed, 02 Jul 1997 10:05:15 +0200 Organization: IGBMC Lines: 46 Message-ID: <33BA0BBB.2F2B@igbmc.u-strasbg.fr> References: <33B26438.3F54@cc.huji.ac.il> <33B42D95.41C6@gcg.com> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) Xref: biosci bionet.software:19014 bionet.software.gcg:2618 > > 6. Edit->Translate, turn on Align Translation, and hit OK. > > Here's where I had the problem: I got a single line of translation, > all in > the reading frame of the first CDS. If I select each CDS separately and > translate it (remembering to select align translation each time -- why > isn't this the default?), it works. > Here I must disagree with you to some extent. Seqlab joins the selected CDS's before it translates and aligns them. Thus it properly takes care of codons splitted by introns when you select all exons simultaneously. If you select separately the exons coding for one single protein, then you may get quite a wrong translated sequence. Let's take the example of L29190 once again. If I do what Steve suggested I get the correct protein sequence aligned to corresponding exons : ...ATGGGGGCGATG (...) ACCCGCGCTG//GTGAG (...) CCCAG//GCTCACACTCGCTGA... ...M~~G~~A~~M~~ (...) T~~R~~A~~G//~~~~~ (...) ~~~~~//~~S~~H~~S~~L~~R... If I select each exon separately though, I get : ...ATGGGGGCGATG (...) ACCCGCGCTG//GTGAG (...) CCCAG//GCTCACACTCGCTGA... ...M~~G~~A~~M~~ (...) T~~R~~A~~X ...~~~~~~~~~~~~ (...) ~~~~~~~~~~//~~~~~ (...) ~~~~~//A~~H~~T~~R~~*~~ ...which, obviously, is not what we want... (// to show splice junctions are mine) Of course, if more than one protein is coded by your genomic sequence, then you'd better select each one separately to avoid the problem you encountered. But, again, all exons for every single protein should be selected simultaneously. In any case though, you should check that the first selected exon is translated in the correct reading frame. Which may not be the case if it is not exon1... In this case, I'm afraid you'll need to select the first exon at the sequence level to exclude the first one or two bases. Cheers, Fred From owner-software@net.bio.net Tue Jul 01 23:00:00 1997 Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology From: John S Walker Subject: Re: Image processing SW X-Nntp-Posting-Host: mars.med.virginia.edu Content-Type: text/plain; charset=us-ascii Message-ID: <33BA6487.7049A250@virginia.edu> Sender: usenet@murdoch.acc.Virginia.EDU Content-Transfer-Encoding: 7bit Cc: trier@pilot.msu.edu Organization: University of Virginia References: <339BE6EB.2C7B@radium.uio.no> <01bc7852$3ab93940$910d20cb@default> <5pb8pi$cs5$1@msunews.cl.msu.edu> Mime-Version: 1.0 Date: Wed, 2 Jul 1997 14:24:07 GMT X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.29 i486) Lines: 50 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!news.comet.net!hearst.acc.Virginia.EDU!murdoch!usenet Terry Trier wrote: > I'm looking for imaging software the runs on a PC (Win 95) that is capable > of measuring the area of several objects at one time, and then summing up > the areas so that you get a total area in a single row in a data file. > > For instance, if I scan 4 tree leaves at once, I want to be able to scan > each leaf, measure the area, and then get a total area. > > Any suggestions? I have tried several 'high-powered' software packages that > seem to be incapable of doing this, yet it is a default and simple operation > for an older, dos-based software that we have. > > Terry M. Trier > Entomology Dept. > Michigan State University > trier@pilot.msu.edu > > Please use the pilot email address. The address in the header is for junk > mail readers. Terry, You might try tnimage a shareware (dos based) image analysis package that is very good and has a scripting language that will let you do what you want. Another package that is Win95 based is imagetool again with a scripting language that will do what you want. Imagetool is freeware (I believe). There is also a PC version of NIH Image (Scion image) that can do it. I am assuming however that you are using background substraction or edge detection to define your closed areas and then summing those areas to get your final result. You might also consider that if you have a tool that does what you want, why change it. Numerous image processing packages that can do what you want and much more are also available under Linux and and both they and Linux are free TN-Image is at http://las1.ninds.nih.gov/ Imagetool is at http://ddsx.uthscsa.edu/dig/itdesc.html Scion Image is at http://www.scioncorp.com/ John Walker Dept of Physiology University of Virginia From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software Subject: Re: ClustalW 1.7 new release - bug ? Date: Thu, 03 Jul 1997 15:10:15 +0100 Organization: SEQNET Lines: 43 Distribution: bionet Message-ID: <33BBB2C7.167E@dl.ac.uk> References: <5p0k7c$bsq@lion.embl-heidelberg.de> <33BBB144.41C6@dl.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) To: Martin Hilbers Martin Hilbers wrote: > > Hi folks, > > So far, the new release of clustalw works fine for me when used > interactively, but if I use command line parameters, like: > > clustalw tmp.seq /gapopen=15.0 /gapext=0.1 > > I get the following error: > > ERROR: Could not open sequence file tmp.seq/gapopen=15.0/gapext=0.1 > > So it seems that it looses the whitespace between the command line > arguments (this was on unix - SGI irix and DEC OSF/1) > > Any suggestions ? Oops - sorry folks.... Just read note 15 of the readme file.. 15. The standard command line separator for UNIX systems has been changed from '/' to '-'. ie. to give options on the command line, you now type clustalw input.aln -gapopen=8.0 instead of clustalw input.aln /gapopen=8.0 Cheers (blushing...) Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!surfnet.nl!newsgate.unisource.nl!fido.news.demon.net!demon!dispatch.news.demon.net!demon!europa.clark.net!newsfeed.sovam.com!sovam!Gamma.RU!srcc!Radio-MSU.net!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: schreuer@u33.num.math.uni-goettingen.de (Peter.Schreuer) Newsgroups: bionet.software Subject: Current-Voltage-Relationships of channels Date: 03 Jul 1997 17:04:59 +0200 Organization: GWDG, Goettingen Message-ID: NNTP-Posting-Host: u33.num.math.uni-goettingen.de X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 5 Hi, I'm looking for programs wich shows I/V relationships of membran channels. Peter From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsxfer.itd.umich.edu!cwis-20.wayne.edu!cmb.biosci.wayne.edu!not-for-mail From: dwomble@cmb.biosci.wayne.edu (David Womble) Newsgroups: bionet.software Subject: Re: clustalw.tar.Z Date: 3 Jul 1997 20:28:31 GMT Organization: Wayne State University Lines: 31 Distribution: world Message-ID: <5ph21f$l14@cwis-20.wayne.edu> References: <33b2d765.2412810@news.rug.ac.be> Reply-To: dwomble@cmb.biosci.wayne.edu NNTP-Posting-Host: cmb.biosci.wayne.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Andy Vierstraete (andy.vierstraete@rug.ac.be) wrote: : TBerke@CHKD.COM ("Berke, Tamas") wrote: : >Dear Colleagues: : >When I try to compile the clustalw files on my machine (Solaris 2.5.1), : >I receive the following message: : >make: Fatal error: Don't know how to make target `clustalw.c` : >Can anyone help me with this problem? : : I had also a lot of problems with installing clustalw. You have to : compile it with 'make -f makefile.sun'. One little problem : it : didn't work. You have to open te file 'makefile.sun' with a text : editor...{snip} The latest version (1.7) I picked up didn't have a makefile.sun file in the package, so I just copied makefile to makefile.sun and edited it so that CC points to gcc: CC = gcc Then run 'make -f makefile.sun' and all is great (Sun Solaris 2.5.1, GNU gcc compiler). The announcement for version 1.7 is elsewhere among these posts. -David -- David D. Womble Phone: 313-577-2374 Center for Molecular Medicine and Fax: 313-577-6200 Genetics, Wayne State University E-mail: dwomble@cmb.biosci.wayne.edu 5047 Gullen Mall, Detroit, MI 48202 http://cmmg.biosci.wayne.edu/ From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software Subject: Re: ClustalW 1.7 new release - bug ? Date: Thu, 03 Jul 1997 15:03:48 +0100 Organization: SEQNET Lines: 25 Distribution: bionet Message-ID: <33BBB144.41C6@dl.ac.uk> References: <5p0k7c$bsq@lion.embl-heidelberg.de> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) To: Toby Gibson Hi folks, So far, the new release of clustalw works fine for me when used interactively, but if I use command line parameters, like: clustalw tmp.seq /gapopen=15.0 /gapext=0.1 I get the following error: ERROR: Could not open sequence file tmp.seq/gapopen=15.0/gapext=0.1 So it seems that it looses the whitespace between the command line arguments (this was on unix - SGI irix and DEC OSF/1) Any suggestions ? - ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!ais.net!newsfeed.direct.ca!portc01.blue.aol.com!newsstand.cit.cornell.edu!NewsWatcher!user From: kk60@cornell.edu (Kiho Kim) Newsgroups: bionet.software Subject: image software Date: Thu, 03 Jul 1997 13:15:10 -0400 Organization: Cornell University Lines: 12 Sender: kk60@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 132 X-newsreader: MT-NewsWatcher 2.2.2 Hi All: I am looking for a Photoshop plug-in that will measure the area of an outline object. A commercial package that I looked at (The Image Processing Tool Kit CD) comes with 50 plug-in, 49 of which I don't really need, and cost $250. NIH Image can do this but it is limited to 8-bit color. Does anyone out there of a cheap (i.e., share- or freeware) that will just measure area using Photoshop? Thanks. -- Kiho Kim (kk60@cornell.edu) Ecology & Systematics Cornell University From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: TBLASTN of new microbial genomes from TIGR Date: 3 Jul 1997 13:31:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707032032.QAA06764@borduas.nlm.nih.gov> Reply-To: francis@ncbi.nlm.nih.gov NNTP-Posting-Host: net.bio.net A new BLAST service for the recently released microbial genomes from The Institute for Genomic Research (TIGR) is now available from the BLAST home page at this URL: http://www.ncbi.nlm.nih.gov/BLAST/ or directly from: http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-tigrbl These unfinished genomes are not yet available in GenBank or Entrez. The genomes are searchable via TBLASTN (a user's protein query vs. a 6-frame translation of the microbial DNA sequences) using the new gapped BLAST algorithm (Altschul et al., 1997, submitted). regards to all, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-feed.inet.tele.dk!news.inet.tele.dk!not-for-mail From: Bo Bergmann <120010312330@post5.tele.dk> Newsgroups: bionet.software Subject: HPLC - WIZARD home page update Date: Fri, 04 Jul 1997 00:05:27 +0200 Organization: DTU Lines: 6 Message-ID: <33BC2227.3D18@post5.tele.dk> NNTP-Posting-Host: ppp341.arh.tele.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02E [da]-TDK20 (Win95; I) CC: Bo, Bergmann The homepage of HPLC - WIZARD has been updated to illustrate the use of the application. Surf by and enlist as beta - tester at: http://home5.inet.tele.dk/daller/index.htm From owner-software@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news.he.net!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!atl-news-feed1.bbnplanet.com!news.bbnplanet.com!news1.usf.edu!!user From: "Wen-Ming Yang" Newsgroups: bionet.software Subject: DNA Strider program! Date: Thu, 03 Jul 1997 23:10:30 +0500 Organization: H Lee Moffitt Cancer Center at USF Lines: 4 Message-ID: <5phpir$kb7$1@news.usf.edu> NNTP-Posting-Host: pc-mrc-4t-1.moffitt.usf.edu Mime-Version: 1.0 Content-Type: text/plain; charset="" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet Mail & News for Macintosh - 3.0 I heard that there is a good and simple program called DNA Strider. Does everyone know where I can get it? Thank you very much. From owner-software@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.sovam.com!sovam!Gamma.RU!srcc!Radio-MSU.net!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!amuelle3 From: amuelle3@gwdu19.gwdg.de (Arne Mueller ) Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Followup-To: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Date: 4 Jul 1997 16:36:41 GMT Organization: GWDG, Goettingen Lines: 47 Distribution: world Message-ID: <5pj8qp$rei$1@gwdu19.gwdg.de> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: gwdu08-fddi.gwdg.de X-Newsreader: TIN [version 1.1 PL8] Xref: biosci bionet.molec-model:1652 bionet.biophysics:3297 bionet.software:19035 Marc Saric (Marc.Saric@rz.ruhr-uni-bochum.de) wrote: : Hi all, : I have a little problem: Recently I stumbled over the nice program : Molscript, written by a man named Dr. Per Kraulis from Sweden. : On several pages dealing with this program, it has been said, that one : must obtain a permission from Dr. Kraulis to download and use Molscript, : and that it is free of charge for academic usage. : I wrote two letters to two different mail-adresses of Mr. Kraulis, but : nothing happened. : Does anyone know the actual adress of Dr. Kraulis or anyone who is in : charge of the program, or does anyone know how to obtain the program : (what to send to which adress or whatever). : Thanks in advance! : -- : Bye, : Marc Saric : Visit http://www.rat.de/marc_saric/ Hello Marc, I found this in my Molscript documentation: Dr. Per Kraulis Center for Structural Biochemistry Karolinska Institute NOVUM S-141 57 Huddinge SWEDEN phone +46 8 608 9266 fax +46 8 608 9290 email pjk@oyster.csb.ki.se good luck, Arne From owner-software@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!webtv.net!uunet!in1.uu.net!194.87.0.28!demos!news.maxwell.syr.edu!News1.Vancouver.iSTAR.net!news.istar.net!hammer.uoregon.edu!leto.ou.edu!news.ou.edu!news.ecn.uoknor.edu!munnari.OZ.AU!news.mel.connect.com.au!news.netspace.net.au!not-for-mail From: Andrew Dyall Newsgroups: bionet.software Subject: Heart software model Date: Fri, 04 Jul 1997 13:52:24 +1100 Organization: Netspace Online Systems Lines: 12 Message-ID: <33BC6568.6411@netspace.net.au> Reply-To: adyall@netspace.net.au NNTP-Posting-Host: dialup-m3-42.melbourne.netspace.net.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) Hi. Has anyone heard of a program that models the electrical acivity of the heart, out-putting in 4 dimensions (3 for direction, one for strength of signal) over time? (I guess that's 5 dimensions overall). Please email me if you have any advice, or know where I should look: adyall@netspace.net.au Thanks, Andrew From owner-software@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!howland.erols.net!torn!hone!informer1.cis.McMaster.CA!wolf.interlynx.net!not-for-mail From: "Lars Thomsen" Newsgroups: bionet.software Subject: Inverting sequences, fast, small and free utility Date: Fri, 4 Jul 1997 03:23:31 -0400 Organization: Interlynx Lines: 11 Message-ID: <5pi8b1$r4h$1@wolf.interlynx.net> NNTP-Posting-Host: port2.hm.interlynx.net X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Hi I have created a little utility that loads as fast as notepad and takes any sequence (no limit in size) and inverts it. You can paste, copy and cut as you want.. If anybody is interested then I can put it on my website for some time.. Best Regards Lars Thomsen From owner-software@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Marc Saric Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: HOW TO CONTACT THE AUTHOR of Molscript???? Date: 4 Jul 1997 01:14:13 -0700 Organization: Ruhr-University of Bochum Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> Reply-To: Marc.Saric@rz.ruhr-uni-bochum.de NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:1651 bionet.biophysics:3296 bionet.software:19033 Hi all, I have a little problem: Recently I stumbled over the nice program Molscript, written by a man named Dr. Per Kraulis from Sweden. On several pages dealing with this program, it has been said, that one must obtain a permission from Dr. Kraulis to download and use Molscript, and that it is free of charge for academic usage. I wrote two letters to two different mail-adresses of Mr. Kraulis, but nothing happened. Does anyone know the actual adress of Dr. Kraulis or anyone who is in charge of the program, or does anyone know how to obtain the program (what to send to which adress or whatever). Thanks in advance! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ From owner-software@net.bio.net Fri Jul 04 23:00:00 1997 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Sequin 2.14 now available Date: 5 Jul 1997 09:23:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707051624.MAA09351@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net Dear Sequin users, We have recently released a new version of Sequin, the sequence submission/editing tool from NCBI, for all platforms. The current version of Sequin is now 2.14 Please refer to the Sequin home page at: http://www.ncbi.nlm.nih.gov/Sequin/ for the latest developments, new questions in the Frequently Asked Questions section, and the most recent version of the help documentation. The home page also contains a link to the new and much improved version of the Sequin Quick Guide, a step-by-step description of how to prepare your Sequin submission, a must-read for all new and seasoned Sequin users. What was changed for Sequin version 2.14? ----------------------------------------- . Network Entrez, an NCBI tool for accessing bibliographic, sequence, and structure records is now fully integrated into Sequin. As before, users can download sequences from Entrez to view or to edit and resubmit to the databases. Now, users can also view any type of record on demand from within Sequin. Users are reminded that they can only update their own records this way. . PowerBLAST, a version of the client for the popular BLAST software for sequence comparisons, is now available from within Sequin. Users can compare their sequence to sequences in the nucleotide and protein databases and view the from results within Sequin. . A new algorithm is now used to calculate global sequence alignments. You can have Sequin calculate and display the alignment between a sequence in the record and another sequence in a file. In the sequence editor, select the option "Align with" under the Edit menu. . Sequin will now recognize sequence alignments which have been saved in NEXUS Interleaved and NEXUS Contiguous formats. Examples of these formats are in the Sequin help documentation. . Records can now be viewed with two new Display Formats, Summary and Sequence. Summary format shows the range of any sequence alignments in the record. Sequence format shows the sequence(s) in the record along with any associated features. . The location of certain menu items has been changed. All features and descriptors are now accessed from the Annotate menu. . A variety of minor bugs have been fixed (affecting all platforms). Please do not hesitate to let us know (info@ncbi.nlm.nih.gov) if you have any questions or comments. francis, for the sequin development team. -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Sat Jul 05 23:00:00 1997 Message-ID: <33B6B20B.3676661F@teneri.step.es> Date: Sun, 29 Jun 1997 19:05:47 +0000 From: Angel Vidal X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.0 i586) MIME-Version: 1.0 Newsgroups: bionet.software Subject: ECG Files required Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: tfrem4.step.es X-NNTP-Posting-Host: tfrem4.step.es Organization: STEP On Line ( http://www.step.es ) Lines: 16 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!howland.erols.net!surfnet.nl!news.unisource.nl!News.Amsterdam.UnisourceCS!newsfeed.mad.ibernet.es!news.step.es!tfrem4.step.es Hello, I'm an studient of telecommunications and I'm working in a electromedical project. I'm designing a digital filter for ecg fetal signals. I need files with this data type. If anybody can helpme please emailme or post this message, thanks, Angel -- ____________________________________ Angel Vidal Hernandez c/Ulises Guimera Castellano 4, bj. C 38001 S/C de Tenerife Canary Islands SPAIN tlph: 34-22 242033 http://www.step.es/personales/aevidal ____________________________________ From owner-software@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!xfer.kren.nm.kr!nntp.kreonet.re.kr!newsfeed.kreonet.re.kr!usenet.seri.re.kr!bioneer.kaist.ac.kr!yshan From: yshan@bioneer.kaist.ac.kr (Yoonsoo Hahn) Newsgroups: bionet.software Subject: [Q] C function library which can handle GenBank flat file? Date: 6 Jul 1997 07:23:23 GMT Organization: Dept. of Biological Sciences, KAIST Lines: 9 Message-ID: <5pnh5b$6sl$1@green.kreonet.re.kr> NNTP-Posting-Host: bioneer.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] Dear netters, I need a C function library which can read GenBank feature table and extract sequnece fragments. For example, it should be able to read mRNA tag, read fragment positions, and extract fragments. Is there any software or C module which can do it? Y. Hahn -- From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!trevor From: trevor@leland.stanford.edu (Trevor Bezdek) Newsgroups: bionet.software Subject: genbank ORFs > fasta ?? Date: Sun, 06 Jul 1997 20:57:45 -0700 Organization: Stanford University Lines: 17 Message-ID: NNTP-Posting-Host: 171.65.20.254 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Is there any program out there that converts files in standard genbank nucleotide format into a fasta file with all of the ORF translations? All of the information is in the file, it would just be a pain to do it by hand. Otherwise, is there any copies of the E.coli genome with the translated ORFs in fasta form? thanks, trevor bezdek -- Trevor Bezdek Department of Developmental Biology Stanford University School of Medicine Beckman Center B343 Stanford, CA 94305-5427 trevor@cmgm.stanford.edu From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news.corp.sgi.com!enews.sgi.com!EU.net!newsfeed.internetmci.com!news.telstra.net!harbinger.cc.monash.edu.au!newshost.carno.net.au!surya From: Shoba.Ranganathan@anu.edu.au (Shoba Ranganathan) Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Date: Sun, 29 Jun 97 20:49:02 GMT Organization: JCSMR,ANU Lines: 43 Distribution: world Message-ID: <5ppa6u$46p$1@clarion.carno.net.au> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: 150.203.193.135 X-Newsreader: News Xpress Version 1.0 Beta #4 Xref: biosci bionet.molec-model:1657 bionet.biophysics:3305 bionet.software:19046 In article <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de>, Marc Saric wrote: >Hi all, > >I have a little problem: Recently I stumbled over the nice program >Molscript, written by a man named Dr. Per Kraulis from Sweden. >On several pages dealing with this program, it has been said, that one >must obtain a permission from Dr. Kraulis to download and use Molscript, >and that it is free of charge for academic usage. > >I wrote two letters to two different mail-adresses of Mr. Kraulis, but >nothing happened. > >Does anyone know the actual adress of Dr. Kraulis or anyone who is in >charge of the program, or does anyone know how to obtain the program >(what to send to which adress or whatever). > >Thanks in advance! Dear Marc, Per Kraulis is currently with Pharmacia - however, you can ask for permission to copy Molscript from anyone who has a registered version and send Kraulis e.mail to that effect ("Per Kraulis" ). The source code is made available (in Fortran) and you can then compile it for your machine. Please contact me if you wish to copy the program from us. Shoba =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)============== From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!128.223.220.26!arclight.uoregon.edu!leto.ou.edu!news.ou.edu!news.ecn.uoknor.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!news.deakin.edu.au!okda15 From: Rkarthi@deakin.edu.au (Karthi Ramachandran) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for windows Date: Sun, 06 Jul 97 23:51:17 GMT Organization: Deakin University Lines: 29 Message-ID: <5ppb63$6gp$1@miranda.its.deakin.edu.au> References: <5n6od4$6lf@ccshst05.cs.uoguelph.ca> <19970615142800.KAA21232@ladder02.news.aol.com> <33B25500.C76@well.com> NNTP-Posting-Host: okda15.bcs.deakin.edu.au X-Newsreader: News Xpress 2.0 Beta #2 >you mighe also try WinPlas from Goldstein Software at $325, and Gene >Runner from Hastings software in the 400-500 price range. email me at >alsbyte1@earthlink.net if you need more info. >Best regards, >Betsy Alberty Hi Betsy, Could you please provide me with more info on hastings software. I have a win3.1 ver of Generunner which I purchased when I was in Canada. I like its performance in DNA manupulations but it has prcatically no plasmid drawing capabilities. I am wondering if they have released a more advanced win95 version. Could you send me theit Fax/www address. Thanx very much for your help. Karthi. R Please remove the R in the begining of my e-mail address to reply directly to me. The R is a Spamblock in my address....Thanx ;-) ------------------------------------------------------------------------------- Karthikeyan Ramachandran Ph.D Research Fellow, Rm. No. SA136 School of Biological and Chemical Sciences Faculty of Science and Technology Phone (Off) 61 (3) 5227 1406 Deakin University Phone (Res) 61 (3) 5241 9806 Geelong, Victoria Fax 61 (3) 5227 2022 Australia 3217 e-mail karthi@deakin.edu.au Home page http://www.deakin.edu.au/~karthi/ From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Newsgroups: bionet.software,bionet.molbio.genbank Path: biosci!rutgers!gatech!howland.erols.net!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!129.174.1.8!portal.gmu.edu!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: perl extraction of protein sequence X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.3/Emacs 19.34 Date: Fri, 4 Jul 1997 15:25:06 GMT Lines: 5 Xref: biosci bionet.software:19050 bionet.molbio.genbank:2666 I am looking for a perl script to read a Genbank file and build a file of the translation products. Bill Pearson From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!howland.erols.net!usc!chi-news.cic.net!199.242.16.13!news4.ixa.net!ixa.net!uunet!not-for-mail From: HOTPUSSY@alpin.or.at Newsgroups: bionet.software Subject: <<>> Date: 7 Jul 1997 17:37:57 GMT Organization: YOUNGXXXPUSSY Lines: 12 Message-ID: <5pr9hl$dag@news0-alterdial.uu.net> NNTP-Posting-Host: 1cust56.max14.los-angeles.ca.ms.uu.net I found a secret password that lets you into 1800+ of the Hottest Adult Sites on the Web. You can also get FREE UNLIMITED Live Video Sex and FREE XXX Chat Room Access. I no longer pay to get into Adult Sites... you won't either. This secret password gets you into them for FREE. http://38.216.112.100/password From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: genbank ORFs > fasta ?? [readseq note] Date: 7 Jul 1997 14:43:26 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <5pqvae$9hd$1@dismay.ucs.indiana.edu> References: <199707070451.AAA10876@borduas.nlm.nih.gov> NNTP-Posting-Host: chipmunk.bio.indiana.edu The current readseq will not do feature table parsing nor the requested ORF cutting and pasting. It doesnt' have any particular file or sequence size limit, so it probably will convert from genbank to fasta formats okay for large sequences. I am working on a new version of readseq in conjuntion with a new SeqPup. It will likely come in C++ and Java source, but not C source. I've no idea when this updated readseq may be available. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!in2p3.fr!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.software Subject: Free practical programs for molecular biologists !!! Date: Mon, 07 Jul 1997 16:15:22 +0200 Organization: University of Zurich Lines: 49 Message-ID: <33C0F9F9.7B45@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=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I wrote a few practical and simple to use programs which facilitate your daily work in the lab such as predicting the size of DNA fragments after digestion (graphical) with restriction enzymes. I would like to make these programs accessible to a broad user group by the Internet. All programs have been tested on MacOS and Windows95. My programs are accessible over the WWW and made functional using Netscape 2.x or Internet Explorer 2.x or higher in association with a free plugin which you have to download and install first. This is what you do: - Download the Roadster plugin http://www.unizh.ch/vetvir/plugin.html) install it on your computer. - Then connect to: http://www.unizh.ch/vetvir/programs.html That's it !! These are my programs which make your live as a molecular biologist easier ! Find here a few more examples or my programs: a. Digest Preview: Enter the size(s) of your DNA fragment(s) and see their migration pattern in a virtual gel in comparison to a 1 kb ladder. b. Adapter Design: Helps to create in frame adapters in order to link incompatible DNA ends together. c. Dilution Calculator: Does all the calculations when you have to make up solutions There are many other programs such as Oligo Tm, Compatible ends etc. Please have a look, comments are welcome! Have fun Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!dispatch.news.demon.net!demon!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!bentley!deleage From: deleage@bentley (Christophe Geourjon) Newsgroups: bionet.software Subject: ANTHEPROT 3.0 for windows available Date: 7 Jul 1997 13:47:23 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Message-ID: <5pqs1b$nu9@cri.ens-lyon.fr> NNTP-Posting-Host: ibcp.fr X-Newsreader: TIN [version 1.2 PL1] Lines: 64 ========================================================================== The latest release of ANTHEPROT 3.0 for Windows is now available by anonymous ftp to ftp.ibcp.fr. ========================================================================== ANTHEPROT software for Windows ANalyze THE PROTein Copyright 1995-1997 This program is developed in the : Institut de Biologie et Chimie des Proteines IBCP-CNRS UPR 412 Laboratoire de conformation des prot‚ines 7, Passage du vercors 69 367 Lyon cedex 07 France Tel : (33) 72 72 26 47 Fax : (33) 72 72 26 01 deleage@ibcp.fr Don't hesitate to contact me in case of problems, bugs or suggestions. The ANTHEPROT package permits the analysis of a protein sequence and 3D structure analysis in a single interactive program: The main methods yet available * Study of physico-chemical properties: hydrophobicity, antigenicity, flexibility, solvent accessibility, amphiphilicity. * Matrix dot plots * Multiple alignment : Multalin, Clustal,Clustalw * Search for biological sites using PROSITE * Search for homologous protein : Program FASTA (W. Pearson) * Secondary structure prediction: Garnier,Gibrat, Deleage, Levin. * Prediction of transmembranous regions & of structural domains. * Look and handle 3D protein structures from PDB files. * Tools: Editor, File, Printing, format, colors ... and much more.... ========================================================================== Here are the latest improvements the software: * fix in stupid bug of calculating perfect matches * Interactive graphic editor for Multiple alignments (Clustalv, ClustalW and Mulatlin formats) * Possibility of exporting alignments into Rich Text Format (rtf) allowing the alignment to be read in color from main Word processors * Nice alignment printing with various text attributes. * Predicted secondary structure visible within multiple alignment * Conformational score of secondary structure (H,E,T,C) can be obtained by double click onto the sequence name from within multiple alignment To appear in next major release * addition of other methods (protein digestion,...) * antigenicity prediction methods * .... =================================================================== Institut de Biologie et Chimie des Proteines. UPR 412-CNRS ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # 7, passage du Vercors # ***** # # # 69367 Lyon Cedex 07,FRANCE # # # # #**** Tel: (33) 04-72-72-26-47 # # # # # # Fax: (33) 04-72-72-26-01 ***** ****** **** # deleage@ibcp.fr From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!kazusa.or.jp!miyajima From: miyajima@kazusa.or.jp (Nobuyuki Miyajima) Newsgroups: bionet.software Subject: Re: perl extraction of protein sequence Date: 7 Jul 1997 07:09:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 69 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707071410.XAA06383@not1.kazusa.or.jp> NNTP-Posting-Host: net.bio.net From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: perl extraction of protein sequence Date: Fri, 4 Jul 1997 15:25:06 GMT > > I am looking for a perl script to read a Genbank file and build > a file of the translation products. > > Bill Pearson > Please try this. Nobuyuki Miyajima ----------------------------------------------- Kazusa DNA Research Institute Department of Genome Informatics, Chief Researcher 1532-3 Yana, Kisarazu, Chiba 292, Japan TEL: +81-438-52-3917 FAX: +81-438-52-3918 E-mail: miyajima@kazusa.or.jp ====================================================== #!/usr/local/bin/perl $infile = shift; $file = $infile; $file =~ s#\.gb_pr##; # GCG $file =~ tr#a-z#A-Z#; $word = ""; $counter = 0; open(IN,$infile) || die "Cannot open $infile"; while(){ chomp; s#^(\s|\t| )*##; m#^CDS# && ($check = 1); if($check == 1){ if(m#^\/translation=\"(.+)#){ $word .= $1; $check = 2; if($word =~ m#\"$#){ $check = 0; $word =~ s#\"$##; } } else{ next; } } elsif($check == 2){ $word .= $_; if($word =~ m#\"$#){ $check = 0; $word =~ s#\"$##; } } else{ next; } } close(IN); print ">$file\n"; @chars = split(//,$word); foreach $char (@chars){ print "$char"; $counter++; if($counter == 70){ $counter = 0; print "\n"; } } ($counter != 0) && (print "\n"); From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!U.WASHINGTON.EDU!egn From: egn@U.WASHINGTON.EDU ("E. Kolker") Newsgroups: bionet.software Subject: CALL FOR PAPERS: Recomb 98 Date: 7 Jul 1997 11:50:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 193 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net CALL FOR PAPERS SECOND ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 98) March 22 - 25, 1998 New York City Sponsored by Association for Computing Machinery SIGACT with support from SLOAN Foundation US Department of Energy http://www.mssm.edu/biomath/recomb98.html The Second Annual Conference on Research in Computational Molecular Biology (RECOMB 98),sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, and US Department of Energy will be held in New York City, March 22 - 25, 1998. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Pavel Pevzner RECOMB 98 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by October 20, 1997. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 98. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 15, 1997. A final copy of each accepted paper is required by January 10, 1997. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. Conference Events RECOMB 98 will feature 8 invited lectures (to be announced later) by prominent biologists including the following conference events: THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS. The Stanislaw Ulam Memorial Lecture awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. THE DISTINGUISHED CONFERENCE LECTURE. The conference will start with the Distinguished Conference Lecture awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE. A lecture describing emerging, new technologies. BEST PAPER BY A YOUNG SCIENTIST AWARD. This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 2 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. STEERING COMMITTEE: Sorin Istrail, RECOMB General Vice-Chair (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California) PROGRAM COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson (Mount Sinai School of Medicine) Bonnie Berger (MIT) Martin Farach (Rutgers University) Phil Green (University of Washington) Dan Gusfield (University of California, Davis) David Haussler (University of California, Santa Cruz) Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Minoru Kanehisa (Kyoto University, Japan) Eugene Koonin (National Center for Biotechnology Information) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Pavel Pevzner, Program Committee Chair (University of Southern California) David Searls (SmithKline Beecham) Ron Shamir (Tel-Aviv University, Israel) Terry Speed (University of California, Berkeley) Martin Vingron (German Cancer Center) Michael Waterman (University of Southern California) ORGANIZING COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson, Conference Chair (Mount Sinai School of Medicine) Martin Farach (Rutgers University) Eugene Kolker, Publicity Chair (University of Washington) Information about local arrangements can be obtained by consulting the conference web page http://www.mssm.edu/biomath/recomb98.html or from the Conference Chair: Professor Gary Benson Department of Biomathematical Sciences Box 1023 The Mount Sinai Medical Center One Gustave L. Levy Place New York, NY 10029-6574 (212) 241-5777 phone (212) 860-4630 fax benson@ecology.biomath.mssm.edu From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: genbank ORFs > fasta ?? Date: 6 Jul 1997 21:50:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707070451.AAA10876@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From trevor@leland.stanford.edu Mon Jul 7 00:18:38 1997 > Is there any program out there that converts files in standard genbank > nucleotide format into a fasta file with all of the ORF translations? All > of the information is in the file, it would just be a pain to do it by > hand. Trevor, there is readseq (from Don Gilbert), but I doubt it will work on the E.coli genome! If you do a www search with "gilbert readseq" you will get quite a few hits! Here is one possibility: ftp://iubio.bio.indiana.edu/molbio/readseq/ (but there are many other implementation on the www) > Otherwise, is there any copies of the E.coli genome with the > translated ORFs in fasta form? yes, we maintain these at NCBI, as we have them as blastable databases. for our various BLAST serveices See: ftp://ncbi.nlm.nih.gov/blast/db/ecoli.aa.Z and: ftp://ncbi.nlm.nih.gov/blast/db/ecoli.nt.Z These are the sequences from Fred Blattner's group. regards, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!news.bc.net!dragon.sk.sympatico.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: genbank ORFs > fasta ?? Date: Mon, 07 Jul 1997 15:04:07 -0500 Organization: University of Manitoba Lines: 30 Message-ID: <33C14BB7.369B@cc.umanitoba.ca> References: <199707070451.AAA10876@borduas.nlm.nih.gov> NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4u) > From trevor@leland.stanford.edu Mon Jul 7 00:18:38 1997 > Is there any program out there that converts files in standard genbank > nucleotide format into a fasta file with all of the ORF translations? All > of the information is in the file, it would just be a pain to do it by > > hand. > > Trevor, The FEATURES program from the XYLEM package can parse any annotated GenBank features from any GenBank file or set of files. Output is in Fasta format. For more information see: http://home.cc.umanitoba.ca/~psgendb/XYLEM.html -- =============================================================================== Brian Fristensky | Department of Plant Science | To really appreciate the magnitude of University of Manitoba | 1997 Red River Valley flood, Winnipeg, MB R3T 2N2 CANADA | consider this: not even CANADA CUSTOMS frist@cc.umanitoba.ca | could stop it from crossing the border! Office phone: 204-474-6085 | FAX: 204-474-7528 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!news-was.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!tubsibr!rzlimes.gbf-braunschweig.de!not-for-mail From: "Dr. Thomas Heinemeyer" Newsgroups: bionet.software Subject: TRANSFAC 3.2 Date: Tue, 08 Jul 1997 08:43:58 +0200 Organization: Ges. f. Biotechn. Forsch. mbH (non profit) Lines: 86 Message-ID: <33C1E1AE.111F@gbf-braunschweig.de> NNTP-Posting-Host: gen219.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) TRANSFAC 3.2 is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzold's SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several sequence analysis tools such as - PatSearch, which uses the sequence information contained in the SITE table for analysis of submitted sequences, - MatInspector, using a library of matrices selected from the TRANSFAC MATRIX table (see Quandt et al., Nucleic Acids Res. 23:4878-4884, 1995). Moreover, the TRANSFAC server provides a new program (SaGa: structural analysis with genetic algorithms, developed by Stefan Meier) which can be used to identify structural characteristics in the environment of aligned functional sites, e.g., transcription factor binding sites. SaGa uses a library of structural parameters developed by H. Sklenar and coworkers (MDC, Berlin; see Karas et al., CABIOS 12:441-446, 1996). The SRS5 system implemented on the TRANSFAC server comprises the following databases, in addition to the TRANSFAC tables: EMBL, EMBLNEW SWISSPROT, SWISSNEW TREMBL REMTREMBL SPTREMBL PIR EPD PDB PROSITE ENZYME EMBLNEW is now updated daily on the TRANSFAC SRS-Site with the new files from European Bioinformatics Institute (EBI) in Hinxton. Edgar Wingender Thomas Heinemeyer -- Thomas Heinemeyer Tel.: ++49(0)531 6181 295 Ges. f. Biotechn. Forsch. mbH Fax: ++49(0)531 6181 266 Abt. Genomanalyse E-Mail: thh@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/Staff/thh.html D-38124 Braunschweig From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!europa.clark.net!newsfeed.internetmci.com!vixen.cso.uiuc.edu!news.indiana.edu!sunflower.bio.indiana.edu!not-for-mail From: wfischer@sunflower.bio.indiana.edu (Will Fischer) Newsgroups: bionet.software,bionet.molbio.genbank Subject: Re: perl extraction of protein sequence Followup-To: bionet.software,bionet.molbio.genbank Date: 8 Jul 1997 13:30:35 GMT Organization: Biology, Indiana University - Bloomington Lines: 19 Message-ID: <5ptfdr$ekk$1@dismay.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.software:19060 bionet.molbio.genbank:2671 William R. Pearson (wrp@alpha0.bioch.virginia.edu) wrote: : : I am looking for a perl script to read a Genbank file and build : a file of the translation products. You want to extract the translation supplied by GenBank, right? My script to do this is available via the following URL: http://www.bio.indiana.edu/~wfischer/Perl_Scripts/#gbgettrans (to do the translation, see #nt2aa in the same document). -- ____________________________________________________________ Will Fischer Biology Department wfischer@indiana.edu Jordan Hall http://www.bio.indiana.edu/~wfischer Indiana University Lab: 812-855-2549 Bloomington, Indiana 47405 USA FAX: 812-855-6705 From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 From: richard_steinman@cmagroup.com Newsgroups: comp.jobsoffered,bionet.software Subject: USA, KS, Kansas City; Software Engineer; Embedded, C, 68000 assembly Date: 8 Jul 1997 15:44:11 GMT Organization: Career Marketing Associates Lines: 38 Message-ID: <5ptn8b$t2u$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.4 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!sleet.snowhill.com!news.greennet.net!thoth.nilenet.com!natasha.rmii.com!news1.rmi.net!not-for-mail USA, KS, Kansas City; Software Engineer; Embedded, C, 68000 assembly This candidate will work with a highly motivated team in the development of software for embedded instrumentation/monitoring systems. The position included utilizing structured analysis and design methodologies in the design, development, implementation and verification of system software. Additional the position requires strong written and verbal skills and the ability to effectively interact within a cross functional team environment. DUTIES: Analyzes software requirements to determine feasibility of design within time and cost constraints. Consults with hardware engineers and other engineering staff to evaluate interface between hardware and software, and operational and performance requirements of overall system. Utilizes structured analysis and design to develop detailed design documentation and test plans. Reviews or leads review of designs and tracks issues to closure. Develops and verifies software which meets the requirements of the design. Insures all work activities comply with regulatory requirements. QUALIFICATIONS: 5+ years experience in real time embedded multitasking system software development. BS EE or CS. Solid C and 68000 Assembly language skills. Experience in developing software from low level drivers through to the application layer. Understanding of structured analysis and design and its application desirable. Experience in Windows or Windows NT development environment desirable. Salary $55-65,000+ Please refer to JO# 1055RJS in your response. Richard Steinman Team Leader rjs@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!gatech!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!mangalam From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: image software Date: Tue, 08 Jul 1997 13:59:10 -0800 Organization: Dev+Cell Biology, UC Irvine Lines: 25 Message-ID: References: NNTP-Posting-Host: skink.bio.uci.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article , kk60@cornell.edu (Kiho Kim) wrote: > Hi All: > I am looking for a Photoshop plug-in that will measure the area of an > outline object. A commercial package that I looked at (The Image > Processing Tool Kit CD) comes with 50 plug-in, 49 of which I don't really > need, and cost $250. NIH Image can do this but it is limited to 8-bit > color. Does anyone out there of a cheap (i.e., share- or freeware) that > will just measure area using Photoshop? Thanks. Am I missing something or can you not just convert the image to 8bit to do your measurements and use NIH Image? You're not measuring 'sum-of-pixel-values' are you? - You just want to count the # of pixels included. If your time is an issue, then maybe you should consider buying the pkg you mention. hjm -- Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.internetmci.com!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.rediris.es!news.cica.es!bioq13.cie.uma.es!user From: user@myhost.us (Manuel G. Claros) Newsgroups: bionet.info-theory,bionet.software Subject: Re: Review articles on bioinformatics Date: Tue, 08 Jul 1997 16:59:21 +0200 Organization: Universidad de Málaga Lines: 16 Distribution: bionet Message-ID: References: <5p04dl$s37@mserv1.dl.ac.uk> NNTP-Posting-Host: bioq13.cie.uma.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Xref: biosci bionet.info-theory:5337 bionet.software:19066 > In article <5p04dl$s37@mserv1.dl.ac.uk>, writes: > |> Dear Netters: > |> > |> Could any one provide me some references of recent review articles on > |> bioinformatics? Thanks a lot! The last "current opinion in struct biol" (june 97) has a review about software predicting N-terminal sorting sequences. Perhaps this can help you. Best regards -- Manuel G. Claros, Ph.D. claros@uma.es Bioquímica y Biología Molecular Facultad de Ciencias Universidad de Malaga E-29071 Málaga (Spain) From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.maxwell.syr.edu!cam-news-hub1.bbnplanet.com!cam-news-feed3.bbnplanet.com!news.bbnplanet.com!news.inc.net!news.itis.com!pkuzmic From: pkuzmic@biokin.com (Petr Kuzmic) Newsgroups: bionet.software Subject: Freeware program DYNAFIT update Date: Tue, 08 Jul 1997 19:48:18 GMT Organization: BioKin Consulting Lines: 50 Sender: reguser@m4.itis.com Message-ID: <5pu57d$dlr$5@bill.itis.com> Reply-To: pkuzmic@biokin.com NNTP-Posting-Host: m4.itis.com X-Newsreader: News Xpress 2.01 This is a message to all users of program DYNAFIT ----------------------------------------------------------------- DynaFit executable files (PowerMac, DOSbox under Win31,Win95,WinNT) were updated to version 2.16[f]. Improvements were made in the module for automatic determination of confidence intervals for rate constants. An example problem was added, based on experimental data published in [1]. This paper contains 97 differential and algebraic equations and three mathematical appendices that describe the kinetics of competitive binding in the system thrombin-dehydrothrombin-hirudin. Nevertheless, this complicated formal treatment is based on several simplifying assumptions; the fitting parameters are composite or derived kinetic constants. In contrast, in DYNAFIT [2] the kinetic problem is formulated simply by using the following text: [mechanism] E + L <===> EL : k1 k2 F + L <===> FL : k3 k4 where E is thrombin, F is chemically modified thrombin, and L is hirudin. The analysis is completely general, not resting on any assumptions except the mass action law. The adjustable parameters in the fitting model are microscopic rate constants k1-k4, not composite or derived kinetic constants. The executable files and the expanded test files can be downloaded from http://www.biokin.com/dynafit/files/. References: [1] Wedemeyer W.J., Ashton R.W., and Scheraga H.A. (1997) "KINETICS OF COMPETITIVE BINDING WITH APPLICATION TO THROMBIN COMPLEXES" Anal. Biochem. 248, 130-140. [2] Kuzmic, P. (1996) "PROGRAM DYNAFIT FOR THE ANALYSIS OF BIOCHEMICAL DATA: APPLICATION TO HIV PROTEASE" Anal. Biochem. 237, 260-273. ----------------------------------------------------------------- pkuzmic@biokin.com | http://www.biokin.com | fax 608.256.1269 ------------------------------------------------------- Petr Kuzmic, Ph.D. * http://www.biokin.com B i o K i n, Ltd. * P.O. Box 8336 * Madison WI 53708 voice 608.256.4790 * fax 608.256.1269 From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.nacamar.de!nntp.uio.no!mn6.swip.net!mn5.swip.net!news From: Dennis Nilsson <7341@iname.com> Newsgroups: bionet.software Subject: Mac-PC-Disk-Conversion??? Date: Tue, 08 Jul 1997 21:54:53 +0200 Organization: - Lines: 3 Message-ID: <33C29B0D.E19B5AA@iname.com> NNTP-Posting-Host: dialup173-2-24.swipnet.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: s-264289 X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Please help me i need a program wisch can read or convert Mac-files on a pc!!! From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!sol.net!newsfeeds.sol.net!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: genbank ORFs > fasta ?? [readseq note] Date: 8 Jul 1997 17:07:51 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 28 Message-ID: <5pts57$jrd@gap.cco.caltech.edu> References: <199707070451.AAA10876@borduas.nlm.nih.gov> <5pqvae$9hd$1@dismay.ucs.indiana.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <5pqvae$9hd$1@dismay.ucs.indiana.edu>, you write: >I am working on a new version of readseq in conjuntion with a >new SeqPup. It will likely come in C++ and Java source, but not >C source. Ugh, double ugh, no, triple ugh. PLEASE check the C++ version on multiple compilers before releasing it. I've had miserable luck porting C++ code to run outside of the original compiler (/platform) environments. In fact, the situation is so bad that I currently consider C++ to be a nonportable language. Take the average g++ program and try to build it with DEC C++ (Unix or OpenVMS), you'll succeed maybe 10% of the time. Even C++ packages that are carefully maintained to be cross platform, such as Amulet, won't work from release to release on some compilers (ie, the new Metrowerks for Mac/Windows will no longer build it.) Java is by design portable, but on the flip side, is slower than molasses for anything big. So the Java version will probably be ok for a single sequence conversion, but I'd hate to have to funnel a few thousand conversions through a Java readseq. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ************************************************************************** *Affordable VMS? See: http://seqaxp.bio.caltech.edu:8000/www/pcvms.html * ************************************************************************** From owner-software@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!sunflower.bio.indiana.edu!not-for-mail From: wfischer@sunflower.bio.indiana.edu (Will Fischer) Newsgroups: bionet.software Subject: Re: genbank ORFs > fasta ?? Date: 8 Jul 1997 13:34:10 GMT Organization: Biology, Indiana University - Bloomington Lines: 17 Message-ID: <5ptfki$ekk$2@dismay.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Trevor Bezdek (trevor@leland.stanford.edu) wrote: : Is there any program out there that converts files in standard genbank : nucleotide format into a fasta file with all of the ORF translations? All : of the information is in the file, it would just be a pain to do it by : hand. My perl script for this task ("gbgettrans") is available at http://www.bio.indiana.edu/~wfischer/Perl_Scripts/ -- ____________________________________________________________ Will Fischer Biology Department wfischer@indiana.edu Jordan Hall http://www.bio.indiana.edu/~wfischer Indiana University Lab: 812-855-2549 Bloomington, Indiana 47405 USA FAX: 812-855-6705 From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.nacamar.de!fu-berlin.de!news.th-darmstadt.de!news.uni-mainz.de!not-for-mail From: "Dr. Klaus Eimert" Newsgroups: bionet.software Subject: Q:how to save as .gb from .html ? Date: Wed, 09 Jul 1997 11:11:55 +0200 Organization: Dept. of Botany, Geisenheim Research Institute Lines: 29 Message-ID: <33C355DA.C58F2E1F@geisenheim.fa.fh-wiesbaden.de> Reply-To: eimert@geisenheim.fa.fh-wiesbaden.de NNTP-Posting-Host: eimert.fa.fh-wiesbaden.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0 [en] (Win95; I) X-Priority: 3 (Normal) Dear netters, could somebody tell me how to save GenBank sequences displayed in .html format (from searches at the www server) as .gb files, so I can use the to import into other programs and use the feature tables? Any help is greatly appreciated! Regards, Klaus Eimert -------------------------------------------------------------------------------------- Dr. Klaus Eimert Dept. of Botany Geisenheim Research Institute Von-Lade-Str. 1 Phone: + 49 6722 502 469 D-65366 Geisenheim FAX : + 49 6722 502 460 Germany E-mail: eimert@geisenheim.fa.fh-wiesbaden.de -------------------------------------------------------------------------------------- From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.maxwell.syr.edu!nntp.uio.no!mn6.swip.net!seunet!news2.swip.net!mailgate.astra.com!not-for-mail From: Steve Gardner Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Date: Wed, 09 Jul 1997 09:35:11 +0200 Organization: Astra Bioinformatics Centre Lines: 40 Message-ID: <33C33F2F.6B07@draco.se.astra.com> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dpsgr.draco.se.astra.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) To: Marc.Saric@rz.ruhr-uni-bochum.de Xref: biosci bionet.molec-model:1662 bionet.biophysics:3320 bionet.software:19072 Marc Saric wrote: > > Hi all, > > I have a little problem: Recently I stumbled over the nice program > Molscript, written by a man named Dr. Per Kraulis from Sweden. > On several pages dealing with this program, it has been said, that one > must obtain a permission from Dr. Kraulis to download and use Molscript, > and that it is free of charge for academic usage. > > I wrote two letters to two different mail-adresses of Mr. Kraulis, but > nothing happened. > > Does anyone know the actual adress of Dr. Kraulis or anyone who is in > charge of the program, or does anyone know how to obtain the program > (what to send to which adress or whatever). > > Thanks in advance! > -- > > Bye, > > Marc Saric > > Visit http://www.rat.de/marc_saric/ Per Kraulis now works in Luis Parodi's bioinformatics group at Pharmacia & Upjohn in Stockholm. Luis' number is +46 8 695 7759. Good luck. ---------------------------------------------------------------------- Dr Steve Gardner Director Tel: +46 46 33 60 00 Astra Bioinformatics Centre Fax: +46 46 33 71 44 PO BOX 34 E-mail: steve.gardner@draco.se.astra.com S-221 00 Lund Sweden From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 From: Kris Jacobs Newsgroups: bionet.software Organization: Jake's Home Brew Subject: Try Me! NNTP-Posting-Host: 205.139.183.47 Message-ID: <33c1f73c.1@nntp.kalnet.net> Date: 8 Jul 97 08:15:56 GMT Lines: 12 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.47 Hello net world are you a beer drinker or maybe a home brewer than this web page is for you! My web page is dedicated to home brewing and beer on the net! If this interests you than go to Jake's Home (brew) Page it is located at http://www.net-link.net/~jtsnake/ I am looking forward to hearing from you soon!!! Kris Jacobs Jake's Home (brew) Page http://www.net-link.net/~jtsnake/ E-Mail To: jtsnake@net-link.net jtsnake@serv01.net-link.net mpinc@SERV01.NET-LINK.NET From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsxfer3.itd.umich.edu!portc01.blue.aol.com!audrey01.news.aol.com!not-for-mail From: ppspiritop@aol.com (PPSpiritOP) Newsgroups: bionet.software Subject: Daniel--the 7 Thunders! (prophecy diskette) Date: 9 Jul 1997 01:23:52 GMT Lines: 47 Message-ID: <19970709012301.VAA02909@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Daniel--the 7 Thunders! Contents 1. Is Daniel Inspired True Prophecy? (August 1996)* 2. Is Daniel Important?* 3. Daniel 1--Food For Thought 4. Daniel 2--The Stature of an Ancient Statue--1 5. Daniel 2--The Stature of an Ancient Statue--2 6. Daniel 3--Prepare for Persecution and Deliverance 7. Daniel 4--7 Times to Nazi Germany's End!--1 8. Daniel 4--7 Times to Nazi Germany's End!--2 9. Daniel 5--Weighed in the Scales--For Destruction or Deliverance 10. Daniel 6: Prepare for the "Lions' Den" 11. A Fresh Look At Daniel's Time Prophecies* 12. Daniel 7:1-4: The Lion of Judea 13. Daniel 7:5-8: The Bear, Leopard, and Dreadful Beast of Rome 14. Daniel 7:9-22: A Time & a Time and the Judgment 15. Daniel 7:23-25: A Pointed, Horny 3 1/2 Times 16. Daniel 7:23-28: A Pointed, Horny 3 1/2 Times--Again? 17. Who Is Michael?* 18. Daniel 8:1-2: Ram and Goat 19. Daniel 8:13-26: 2300 Years Till Judgment 20. Daniel 8:14, 26: 2300 Years Till 1967 War! 21. Daniel 9:24-27: 70 Weeks--Grand Jubilee 22. Daniel 9:24-27: The Antitypical 70 Weeks 23. Daniel 10: Prince Michael The Mashiach (Messiah) 24. Daniel 11:2-14: Muslim (South) and Christian (North) Kings 25. Daniel 11:15-29: Napoleonic, British, and Nazi Kings of the North 26. Daniel 11:30-45: Father, Napoleonic, and British Kings of the North 27. Daniel 12:1-3: The Time of Trouble & Special Resurrection 28. Daniel 12:4-10: The 2nd 3 1/2 Times and 2nd Time of the End 29. Daniel 12:11: The 1290 Days 30. Daniel 12:12, 13: The 1335 Days. P. W. Phillips, President The Schools of the Prophets The book is available as a diskette in ASCII format. The four starred Daniel-related chapters are free, leaving 26 on Daniel at $1 each. The total price is U. S. $26.00 postpaid. Include your post office address with your order. Send to: The Schools of the Prophets 529 Orchard Street, Suite # 3 Centralia, MO 65240-1200, U.S.A. From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.software Organization: Yankee Inc. Subject: !!!Hello!!! NNTP-Posting-Host: 205.139.183.49 Message-ID: <33c0b454.1@nntp.kalnet.net> Date: 7 Jul 97 09:18:12 GMT Lines: 9 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.49 Are you looking for a great place to find interesting things on the WWW??? Than look no more because you have found the right place!!! The place you are looking for is Yankee Inc.!!! A great Web Site full of interesting links to interesting places!!! Everything from Adult to Xzlyaphone it's here!!! There is something for everyone and then some!!! So give it a try what do you have to lose except some sleep??? Yankee Inc. http://www.kalnet.net/yank714 Yankee Inc. Your Alternative Web Solution!!! Yankee Inc. http://www.kalnet.net/yank714 If you would like to be removed from my mailing list - hit reply and type "REMOVE" and I will promptly remove you from my list!!! Thank You!!! From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!news2.jaring.my!usenet From: "LENNY" Newsgroups: bionet.software Subject: anyone has the crack for internet phone 4.5 Date: 9 Jul 1997 09:50:11 GMT Organization: Unconfigured Lines: 4 Message-ID: <01bc8c4e$03f29ae0$54e38ea1@clone> NNTP-Posting-Host: j6.glg67.jaring.my X-Newsreader: Microsoft Internet News 4.70.1155 hello, if you have the crack for internet phone ver 4.0 or 4.5 please email me at lenny@tm.net.my From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!news.infinet.com!news From: stevev@infinet.com (Steve Cartwright) Newsgroups: bionet.software Subject: Office 95 Professional Date: Wed, 09 Jul 1997 12:06:03 GMT Organization: InfiNet Lines: 11 Message-ID: <33c37c9a.39172068@news.infinet.com> NNTP-Posting-Host: day-tc2-a097.infinet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99f/32.299 Im selling my Office 95 Profesional w\bookshelf(CD Rom) $80.00 I also have "Via Graphix Learning CD Roms for Office 95 Pro. They include Access 95 Introduction,Word 95 Beginner and Advanced,Schedule plus Introduction.The Viagraphix CD's were 49.95 ea I will provide include them in with Office 95 for $12.00 ea. The Above pkg does not include Freight. Thank You E mail Stevev@infinet.com From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Peter Kulmburg Newsgroups: bionet.software Subject: mail with eudora instead of netscape Date: 9 Jul 1997 11:28:25 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5pvp49$enk@mserv1.dl.ac.uk> X-Authentication-Warning: skl1.ukl.uni-freiburg.de: smap set sender to using -f Original-To: bio-software@dl.ac.uk Dear collegues, I have heard about a possibility to use eudora as a mailing program directly when clicking on a "mailto" in netscape. Must I define eudora as a helper application or use a AppleScript protocol? Is there anyone with more details for me? Thank you very much in advance! Sincerely Peter Kulmburg Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 From owner-software@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!news-zh.switch.ch!news.belnet.be!alpha.luc.ac.be!pstn10.luc.ac.be!user From: ghermans@luc.ac.be (Guy Hermans) Newsgroups: bionet.software Subject: Re: Mac-PC-Disk-Conversion??? Date: Wed, 09 Jul 1997 09:13:26 +0100 Organization: Dr. L. Willems-Instituut Lines: 26 Message-ID: References: <33C29B0D.E19B5AA@iname.com> NNTP-Posting-Host: pstn10.luc.ac.be In article <33C29B0D.E19B5AA@iname.com>, Dennis Nilsson <7341@iname.com> wrote: > Please help me i need a program wisch can read or convert Mac-files on a > pc!!! Try using Executor; you can download a free trial version from this Mac system 6 emulator for IBM's. I'm not very much into it myself, but you should be able to copy files to the IBM harddisc with it. Be sure to use shorter names with a correct three-letter extension. But why bother? Mac's can write to an IBM formatted disc; MS Word (and most other programs) can write out their own files to different other types. So you should be able to do it with just the Mac used to create the files. Guy -- Guy Hermans, PhD student Ms research Unit Immunology research group Dr. L. Willems-Institute Dept. of Physiology, LUC University Campus University Campus B-3590 Diepenbeek B-3590 Diepenbeek Belgium Belgium Voice ++32(0)11/26.92.07 Fax ++32(0)11/26.92.09 From owner-software@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!fnews.nuri.net!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!news.clara.net!not-for-mail From: Lloyd Watson Newsgroups: bionet.software Subject: Fungi Identification & Recording Date: Thu, 10 Jul 97 16:30:12 GMT Organization: rn Lines: 35 Message-ID: <970710163012.n0001160.lwatson@mail.clara.net> Reply-To: lwatson@clara.net NNTP-Posting-Host: 194.164.79.70 X-Newsreader: atlantis mail 32 X-No-Archive: yes I have written a Fungi Identification programme, which covers all the higher Fungi of the UK. It is a relational database using English to Maths related tables the core programme is Microsoft Access, I use Access 97 but I can create the programme for all the previous versions. In summary these are the programme features 1. Species Identification using queries pre or self designed. 2. Species Identification using Keys, based on Mosers book. 3. A second user created database recording all the features of a found specimen. 4. Other fields within the database are used for puposes other than identification ie, Rarity, Edible/Poisionous Seasons etc. The programme will record the number of time a species occurs over time indicating local decline/growth. I could go on but I wish to be brief, an article entitled Fungi Identification & Recording System (FIRS) will be printed in the quarterly British Mycological Society magazine, next issue in fact. I wish to gauge the interest in this programme which is near completion. The programme is fininshed and is populated with 2,700 species I have about 300 to go and then some tidying up. I originally never designed it for sale but for my own uses, however it has proved very succesful. I can sell the programme to others who have Microsoft Access as is, if you do not I can sell a runtime version of Microsoft Access with the Fungi programme. This is providing I invest in a developers toolkit. If you are interested and wish to know more mail me at lwatson@clara.net it has taken two years and thousands of hours of work to create this programme so if you expect it to be free don't get in touch. It is likely to be sold to genuine amateur mycologists for 60-70 pounds dependant on the interest. Thank you for your time in reading this article. From owner-software@net.bio.net Wed Jul 09 23:00:00 1997 From: randy97 Subject: http://www.love.com Newsgroups: bionet.software NNTP-Posting-Host: pgh.nauticom.net Message-ID: <33c528e6.0@pgh.nauticom.net> Date: 10 Jul 97 18:24:38 GMT Lines: 9 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!pgh.nauticom.net!pgh.nauticom.net Looking to find people in your area that enjoy the same things as this newsgroup? Check out http://www.love.com It's free, it's new, and it's awesome. Rand From owner-software@net.bio.net Wed Jul 09 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.software Organization: Yankee Inc. Subject: I Am Very Sorry!!! NNTP-Posting-Host: 205.139.183.55 Message-ID: <33c2556c.1@nntp.kalnet.net> Date: 8 Jul 97 14:57:48 GMT Lines: 5 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.55 I would like to apologise to this newsgroup and everyone who reads this newsgroup!!! I promise never to post or send spam to this or any other newsgroup that does not pertain to my posting!!! Please accept my humble apology and again I will never post spam here again!!! Thank You!!! Andrew Schero yank714@kalnet.net From owner-software@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: PubMed: MEDLINE Retrieval on the World Wide Web Date: 10 Jul 1997 14:33:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707102133.RAA13186@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net NOTE: As of June 26, the National Library of Medicine (NLM) is providing free WWW access to its MEDLINE database (see http://www.nlm.nih.gov for further information). Below is the text of the NLM Fact Sheet announcing the PubMed WWW retrieval system (http://www.ncbi.nlm.nih.gov/PubMed). PubMed MEDLINE Retrieval on the World Wide Web PubMed is a World Wide Web retrieval service developed by the National Library of Medicine (NLM). PubMed provides access, free of charge, to MEDLINE, a database of nearly 9 million bibliographic citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences. PubMed also contains links to full text versions of articles at participating publishers' Web sites. PubMed also provides access and links to the integrated molecular biology databases maintained by the NCBI. These databases contain DNA and protein sequences, genome mapping data, and 3-D protein structures. Additional NLM bibliographic databases, such as AIDSLINE, will be added to PubMed. MEDLINE MEDLINE is the NLM's premier bibliographic database, containing citations and author abstracts from over 3800 biomedical journals published in the United States and in 70 foreign countries. Coverage extends back to 1966 and new material is incorporated weekly. All citations in MEDLINE are assigned subject headings from the MeSH vocabulary to assist users in their searches. Searching PubMed PubMed is an easy-to-use search tool for finding journal articles of interest in the health and medical sciences. A basic search screen allows users to search by entering a few key words or phrases. A set of article titles is retrieved and their associated abstracts can be selected for viewing. A unique feature of PubMed is the ability to find all related articles to a given article instantly. Related articles are pre-computed based on textual similarity. Advanced search modes offer the ability to perform more complex searches by specifying data fields and by using Boolean logic to combine multiple search terms. A special clinical query page provides customized searches for studies based on etiology, diagnosis, prognosis, or treatment of a particular disease. Search results can be viewed in various formats, including formats suitable for downloading into bibliographic reference manager software. For journals participating in the PubMed project and which have Web sites, there are links to the full-text of retrieved articles. Note that these links are made to the Web sites of participating publishers and may require users to register before being able to view the full-text. Currently there are 24 full-text journals participating. The URL for PubMed is: http://www.ncbi.nlm.nih.gov/PubMed Publisher Participation Publishers with WWW sites that provided access to the full-text of their journals are invited to participate in PubMed if their journals are already indexed in MEDLINE. Participating publishers supply NLM with formatted citations and abstracts prior to or at the time of publication. In turn NLM creates the PubMed links to the articles at the publishers' sites. NLM also provides citation matching in order to link the citations in the reference section of an article directly back to citations in MEDLINE. Further Information Contact the National Center for Biotechnology Information at (301) 496-2475 or by email at 'info@ncbi.nlm.nih.gov'. The mailing address is: National Center for Biotechnology Information National Library of Medicine Bldg. 38A, Room 8N-803 8600 Rockville Pike Bethesda, MD 20894 From owner-software@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!howland.erols.net!newsxfer.itd.umich.edu!news.mtu.edu!not-for-mail From: huang@mtu.edu (Xiaoqiu Huang) Newsgroups: bionet.software Subject: Analysis and Annotation Email Server Date: 11 Jul 1997 16:29:13 -0400 Organization: Michigan Technological University Lines: 167 Message-ID: <5q652p$foa@string.cs.mtu.edu> NNTP-Posting-Host: string.cs.mtu.edu X-Newsreader: TIN [version 1.2 PL2] The AAT email server at Michigan Tech identifies genes in a DNA sequence by comparing the query sequence against cDNA and protein sequence databases: (1) Human_Gene_Index, a database of human cDNA sequences at TIGR, (2) dbEST, a database of EST sequences at NCBI, (3) SwissProt, a database of protein sequences at University of Geneva, (4) nr, a database of non-redundant protein sequences at NCBI. Author: Xiaoqiu Huang (Email: huang@cs.mtu.edu) Dept. of Computer Science, Michigan Technological Univ., Houghton, MI 49931 The analysis and annotation tool (AAT) includes two sets of programs, one for comparing the query sequence with the protein database, and the other for comparing the query with the cDNA database. Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence. Each alignment program handles the problem of introns. The DNA-protein alignment program corrects frameshifts. The AAT tool reduces the labor-intensive work of locating the exons of the query sequence and improves the process of defining intron/exon boundaries by using the wealth of available protein and cDNA data. Obtaining Help To receive information on using the AAT email server, send a mail message to: aat@cs.mtu.edu Put the word 'HELP' on a single line in the body of the mail message. Examples of Results by AAT A portion of a DNA-protein alignment: Top sequence is the query and bottom one is a database sequence. Accession: SP|P32198|CPT1_RAT MITOCHONDRIAL CARNITINE PALMITOYLTRANSFERASE I Score: 2003 Identity: 482/773 (62%) Strand: plus Script M A E A 62479 GCGCCCGCGCACCCATCTGCCCCCGTCCTAGGTGCCGACCAACCCCCAGGATGGCGGAAG --------------------------------------------------:::::::::: 1 M A E A Script H Q A V A F Q F T V T P D G V D F R L S 62539 CTCACCAGGCCGTGGCCTTCCAGTTCACGGTGACCCCAGACGGGGTCGACTTCCGGCTCA :::::::::::::::::::::::::::::::::::::::::::: ..:::.. ::::::: 5 H Q A V A F Q F T V T P D G I D L R L S Script R E A L K H V Y L S G I N S W K K R L I 62599 GTCGGGAGGCCCTGAAACACGTCTACCTGTCTGGGATCAACTCCTGGAAGAAACGCCTGA ::. ::::::::::::.. ... .::::::::: .. ..:::::::::::: . : 25 H E A L K Q I C L S G L H S W K K K F I EXON 1 62529 62669 CONFIDENCE: 100 66 Script R I K 62659 TCCGCATCAAGGTGCGCACAGGTGCTTCTCCCAGAGCGTAGGCAGAGGCCGGCTGTCAGC ::::: ..:::------------------------------------------------- 45 R F K Script 62719 TGTTAAGCGCTTTGTTAGGGTCCCTCACTGCCTCCTTGGCTGGCACTTCTGCCCGGTACA ------------------------------------------------------------ 48 Script 62779 GGTTGTGGAAGTACAGACACCAGAGGGGTGCACAGGATGTGGTCGGACACAGGGAGCTGT ------------------------------------------------------------ 48 Script 62839 GGGTGTGGCGGAGGAAGGAGCACAGCAGGGCATCAGGAGAGAAAGCCTTCCAGGCCAAGA ------------------------------------------------------------ 48 Script 62899 CCAGGAGCCAGTTCCCAAGACTTCACAGGCAGGCTAACCTCCCGCCTTCCGGCTCCATAA ------------------------------------------------------------ 48 Script N G I L R G V Y P G S P T 62959 GGGCGCCTGTTTCTGCCCACAGAATGGCATCCTCAGGGGCGTGTACCCTGGCAGCCCCAC ----------------------::::::::: ... .::::::. .:::. .. .:::. 48 N G I I T G V F P A N P S Script S W L V V I M A T V G S S F C N V D I S 63019 CAGCTGGCTGGTCGTCATCATGGCAACAGTGGGTTCCTCCTTCTGCAACGTGGACATCTC .::::::::: ..::: .. ... . . . ..::: . ... :::::: .:: 61 S W L I V V V G V I S S M H A K V D P S EXON 2 62981 63120 CONFIDENCE: 60 40 Script L G L V S C I Q R C L P Q G 63079 CTTGGGGCTGGTCAGTTGCATCCAGAGATGCCTCCCTCAGGGGTAAGGAGTGAAACTGGA ::::::: .. .. . ::: .::: .::: . . ------------------ 81 L G M I A K I S R T L D T T A portion of a DNA-cDNA alignment: Top sequence is the query and bottom one is a database sequence. EXON 1 12304 12896 CONFIDENCE: 100 100 12853 TTCACAGACTTCTACGTGCCTGTGTCTCTGTGCACACCCTCTAGGTAAAGAGGGGGCCGC ||||||||||||||||||||||||||||||||||||||||||||---------------- 549 TTCACAGACTTCTACGTGCCTGTGTCTCTGTGCACACCCTCTAG 12913 GCCTCTTCCCCGCCCCGACCCTCCATCCCTTTCCTCCCAATGGATTGCAGGGGGGCGGGA ------------------------------------------------------------ 593 12973 AAAACGTCTGTCTCTCTCTCTAGGGAAGGCCACATTTCTGTCTGTCTCAGGGACTCTGTG ------------------------------------------------------------ 593 13033 ACTTGTCCCGCAGGGCCGCCCTCCTGACCGGCCGGCTCCCGGTTCGGATGGGCATGTACC -------------||||||||||||||||||||||||||||||||||||||||||||||| 593 GGCCGCCCTCCTGACCGGCCGGCTCCCGGTTCGGATGGGCATGTACC 13093 CTGGCGTCCTGGTGCCCAGCTCCCGGGGGGGCCTGCCCCTGGAGGAGGTGACCGTGGCCG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 640 CTGGCGTCCTGGTGCCCAGCTCCCGGGGGGGCCTGCCCCTGGAGGAGGTGACCGTGGCCG 13153 AAGTCCTGGCTGCCCGAGGCTACCTCACAGGAATGGCCGGCAAGTGGCACCTTGGGGTGG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 700 AAGTCCTGGCTGCCCGAGGCTACCTCACAGGAATGGCCGGCAAGTGGCACCTTGGGGTGG 13213 GGCCTGAGGGGGCCTTCCTGCCCCCCCATCAGGGCTTCCATCGATTTCTAGGCATCCCGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 760 GGCCTGAGGGGGCCTTCCTGCCCCCCCATCAGGGCTTCCATCGATTTCTAGGCATCCCGT EXON 2 13046 13286 CONFIDENCE: 100 96 13273 ACTCCCACGACCAGGTAGGAACCACCCGGGCCCTCAGCCACCCTCCCACCTCCCAAAGTC ||||||| ||||||---------------------------------------------- 820 ACTCCCAyGACCAG 13333 CCCCAGCCCTTGATGCTCCCGCAGCCCCACCTGCCAGCCCAGCCCTCACGGCAGCTGCCC ------------------------------------------------------------ 834 13393 GCCTCAGGGCCCCTGCCAGAACCTGACCTGCTTCCCGCCGGCCACTCCTTGCGACGGTGG -------||||||||||||||||||||||||||||-|||||||||||||||||||||||| 834 GGCCCCTGCcAGAACCTGACCTGCTTCC gCCGGCCACTCCTTGCGACGGTGG 13453 CTGTGACCAGGGCCTGGTCCCCATCCCACTGTTGGCCAACCTGTCCGTGGAGGCGCAGCC |||||||||||||||||||||-|||||||||||||||||||||||||||||||||||||| 886 CTGTGACCAGGGCCTGGTCCC aTCCCACTGTTGGCCAACCTGTCCGTGGAGGCGCAGCC 13513 CCCCTGGCTGCCCGGACTAGAGGCCCGCTACATGGCTTTCGCCCATGACCTCATGGCCGA |---|||||-|||||||||||||||||||||||||||||||||-|||||||||||||||| 945 C tGGCT cCCGGACTAGAGGCCCGCTACATGGCTTTCGCC aTGACCTCATGGCCGA EXON 3 13400 13618 CONFIDENCE: 96 96 13573 CGCCCAGCGCCAGGATCGCCCCTTCTTCCTGTACTATGCCTCTCACGTAAGTGATCTTGG ||||-|||||||||||||||||||||||||||||||||||||| ||-------------- 1000 CGCC aGCGCCAGGATCGCCCCTTCTTCCTGTACTATGCCTCTmAC From owner-software@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!129.240.148.41!nntp.uio.no!mn6.swip.net!seunet!news2.swip.net!inet-1.pnu.com!not-for-mail From: Kjell Madsen Newsgroups: bionet.software Subject: Re: Mac-PC-Disk-Conversion??? Date: Fri, 11 Jul 1997 11:05:20 +0200 Organization: Pharmacia & Upjohn Lines: 11 Message-ID: <33C5F74F.C2D1EAD6@eu.pnu.com> References: <33C29B0D.E19B5AA@iname.com> NNTP-Posting-Host: pcmakj.upp.se.pnu.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Dennis Nilsson <7341@iname.com> X-Priority: 3 (Normal) Dennis Nilsson wrote: > Please help me i need a program wisch can read or convert Mac-files on > a > pc!!! Try Conversions Plus http://www.dataviz.com Kjell From owner-software@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!rutgers!gatech!nntprelay.mathworks.com!howland.erols.net!ais.net!News1.Toronto.iSTAR.net!news.istar.net!ftn.net!passport.ca!news From: Christopher Heer Newsgroups: bionet.agroforestry,bionet.plants,bionet.software,sci.bio.botany,bionet.biology.tropical,sci.bio.ecology Subject: In-Field Data Collection Software Date: Fri, 11 Jul 1997 09:21:47 -0400 Organization: Fieldworker Lines: 16 Message-ID: <33C6336B.1D12@fieldworker.com> Reply-To: webmaster@fieldworker.com NNTP-Posting-Host: pm1-10.passport.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Xref: biosci bionet.agroforestry:5870 bionet.plants:16005 bionet.software:19087 bionet.biology.tropical:2636 Introducing a complete range of in-field data collection software linked to GPS. FieldWorker Basic for simple location tagged data. FieldWorker Advanced adds UTM, Laser, Navigation and analytic mapping. FieldWorker Pro for CAD and GIS users: relational data collection and lines and polygons. Find out which version of FieldWorker best suits your needs at http://www.fieldworker.com ================================================================== Christopher Heer, Webmaster A Full Range of In-Field Data Collection Software! Choose from: FW Basic: US$149... FW Advanced: US$599...Coming soon FW Pro!! On-Line Demos! ..."Show Me!"... at http://www.fieldworker.com -- FieldWorker Products Ltd.-- Tel: +1 416 483 3485 ================================================================== From owner-software@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!uunet!not-for-mail From: FREESLUTSXXX@alpin.or.at Newsgroups: bionet.software Subject: Secret Password Gets... 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Date: Sat, 12 Jul 1997 18:31:08 +0100 Message-ID: <868728222.8956.1.nnrp-1.9e989ba8@news.demon.co.uk> NNTP-Posting-Host: kinet.demon.co.uk X-NNTP-Posting-Host: kinet.demon.co.uk [158.152.155.168] X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Lines: 44 If you run a health related Web site then there is now an opportunity to get some money back for all your hard work and provide a useful service to your readers. The Healthworks Shop Partnership Scheme allows participating Web sites to earn commission on sales of medical information products by just adding an extra page to their sites. Healthworks are one of the worlds leading distributors of electronic medical information products, they are Internet trade veterans with over two years experience of selling CD-ROMs and videotapes from their Web site. The partnership deal enables Web sites to make money and provide a useful service to their visitors. For the smaller sites it can earn them enough to cover all their running costs at the least, the more popular sites can create a substantial income for their organisations. Shop Scheme partners can offer the complete range of over 600 medical information products and gain commission on sales of 7-10%. With the average price of a medical CD-ROM at 300, partners make a good profit on each sale. The scheme utilises a commerce system, specially designed by Information Central Limited, to enable simple set-up and administration by anyone with basic HTML skills. The partnership process is simple: 1.Register your interest with Healthworks and a member of staff will view your Web site. 2. If you are approved you will be given simple instructions on how to set up your shop page. 3. A few minutes of HTML programming and you are up and running. 4. Sit back and wait for your monthly sales commissions. To find out more look at the Healthworks Web site at: http://www.healthworks .co.uk/hw/partner/CDpartner.html or e-mail: partners@d-access.demon.co.uk From owner-software@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!BIGFOOT.COM!tnig From: tnig@BIGFOOT.COM (Ti Ng) Newsgroups: bionet.software Subject: FREE Business Opportunities Date: 13 Jul 1997 05:23:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <33C95147.1030@bigfoot.com> Reply-To: tnig@bigfoot.com NNTP-Posting-Host: net.bio.net All you need to make bussines for FREE. FREE BUSINESS and other Opportunities: http://members.tripod.com/~tnigsaul From owner-software@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!newsxfer3.itd.umich.edu!infeed1.internetmci.com!newsfeed.internetmci.com!news.stealth.net!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!usenet From: Andrey Kirillov Newsgroups: bionet.software Subject: Re: Mac-PC-Disk-Conversion??? Date: Sun, 13 Jul 1997 19:51:21 -0700 Organization: Hebrew University Lines: 35 Message-ID: <33C99429.12DC@cc.huji.ac.il> References: <33C29B0D.E19B5AA@iname.com> Reply-To: andreyk@cc.huji.ac.il NNTP-Posting-Host: tova1.md.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Dennis Nilsson wrote: > > Please help me i need a program wisch can read or convert Mac-files on a > pc!!! 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Much more than you can find in any newsgroup. http://home.pi.net/~sappie/playboy.htm From owner-software@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!audrey02.news.aol.com!not-for-mail From: ppspiritop@aol.com (PPSpiritOP) Newsgroups: bionet.software Subject: Daniel prophecy diskette Date: 13 Jul 1997 23:04:43 GMT Lines: 62 Message-ID: <19970713230400.TAA13508@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Daniel--the 7 Thunders! The most complete, comprehensive, thorough, & historically-accurate discussion of chapters 1-12 of the book of Daniel available--resulting from 26 years of personal research & divine aid. Contents (757, 568 bytes; 297 pages--6 1/2" x 9" text area) Table of Contents (2) 1. Is Daniel Inspired True Prophecy?* (4) 2. Is Daniel Important?* (6) 3. Daniel 1--Food For Thought (9) 4. 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