From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: Sequence alignment documentation Date: Mon, 02 Sep 1996 11:57:16 +0100 Organization: Laboratory of Molecular Biophysics Lines: 16 Message-ID: <322ABD8C.41C6@bioch.ox.ac.uk> References: <2016.9608152141@dse> <32142189.A7B@bbsrc.ac.uk> <322803B1.67E0@gardner.demon.co.uk> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Steve Gardner wrote: > > Have you tried Geoff Barton's ALSCRIPT ? > > You can get more info at: > > http://www.mrc-cpe.cam.ac.uk/irbm-course95/gb/docs/alscript/alscript.html > > -- > ---------------------------------------------------------------- > Steve Gardner http://geoff.biop.ox.ac.uk/manuals/ for the full details. Geoff. From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: Sequence alignment documentation Date: Mon, 02 Sep 1996 11:58:44 +0100 Organization: Laboratory of Molecular Biophysics Lines: 12 Message-ID: <322ABDE4.167E@bioch.ox.ac.uk> References: <2016.9608152141@dse> <32142189.A7B@bbsrc.ac.uk> <322803B1.67E0@gardner.demon.co.uk> <322ABD8C.41C6@bioch.ox.ac.uk> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Geoff Barton wrote: > > Steve Gardner wrote: > > > > Have you tried Geoff Barton's ALSCRIPT ? > > http://geoff.biop.ox.ac.uk/manuals/ > > for the full details. > Geoff. Sorry! I meant: http://geoff.biop.ox.ac.uk/manuals.html From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software Subject: Re: GeneDoc address Date: Mon, 02 Sep 1996 09:49:36 +0100 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 17 Message-ID: <322A9FA0.5D7F@bbsrc.ac.uk> References: NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) To: "Marc A. Goldstein" Marc A. Goldstein wrote: I recently upgraded from one computer to another and I would like > to get the latest version of GeneDoc, which does a very nice job of > preparing output from multiple sequence alignements. I no longer have the > URL handy, and was hoping someone out there could post the location. > http://www.cris.com/~ketchup/genedoc.shtml ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.software Subject: Protein Multiple Sequences Editor on IuBio FTP-server Date: 2 Sep 1996 11:21:05 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 49 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50eceh$g1v@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk To: bio-software@dl.ac.uk From: eroshkin@vector.nsk.su Subject: Protein Multiple Sequences Editor on IuBio FTP-server Dear All, ProMSED, Protein Multiple Sequences EDitor for MS Win 3.x/95 is available now from IuBIO software library: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed1.exe (as self-extracted archive). ProMSED is an easy-to-use application for automatic and manual multiple protein sequences alignment, alignment editing, analysis and printing. Interface and the main functions are similar to Microsoft Word. ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, edition and illustrations preparation. Some features: o reads five sequence formats (NBRF/PIR, Pearson (Fasta), EMBL/SwissProt, Intelligenetics and CLUSTAL) and combines sequences from different files; o automatic multiple sequence alignment with ClustalV algorithm; o single and multiple sequence input and edit; o manual alignment includes sequences grouping, blocks deleting, pasting, etc.; o visual analysis is facilitated by amino amino acid coloring reflecting aa similarity in physico-chemical, mutational and other properties; o option for interactive alignment in selected block, leaving unchanged previously aligned regions; o outputs alignment in two formats, produces publication quality alignments; o loads several protein families into different windows; o a HELP is included. Special thanks to Dr. Desmond Higgins for source code of ClustalV. Demo version has limits on length and number of sequences. Comments, bug reports and suggestions for new features are welcome and should be sent by email to eroshkin@vector.nsk.su. Inquiries can be addressed to: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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 Sun Sep 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!burglin From: burglin@ubaclu.unibas.ch Newsgroups: bionet.software Subject: Re: Sequence alignment documentation Message-ID: <1996Sep2.024526.46831@yogi.urz.unibas.ch> Date: 2 Sep 96 02:45:26 MET References: <2016.9608152141@dse> <32142189.A7B@bbsrc.ac.uk> Organization: University of Basel, Switzerland Lines: 63 In article , cas9@cornell.edu (Claudia Sutton) writes: > In article <32142189.A7B@bbsrc.ac.uk>, Andy Phillips > wrote: > >> o.gallay@ic.ac.uk wrote: >> > >> > Hi. >> > Does anyone out there know of a program that will draw a frame around >> > homologous segments of sequence in alignments, ie. like "prettybox" but >> > without the shading? I've often seen this sort of frame in > publications, but >> > everyone I know thinks this has to be done by hand. >> > Please e-mail as well as post! >> > >> >> Genedoc (available from http://www.cris.com/~ketchup/genedoc.shtml) will > output a >> lineup in PICT format, which can (theoretically) be imported into > drawing packages. You >> can then draw your own boxes around conserved regions. In practise, > however, I found >> that CorelDraw6 failed to align the characters properly, and Freelance > crashed on >> importing large lineups. >> >> Andy >> ------------------------------------------------------------------------ >> Email : andy.phillips@bbsrc.ac.uk : University of Bristol >> Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station >> Phone : +44-1275-549257 : Long Ashton >> Fax : +44-1275-394281 : Bristol, BS18 9AF, UK >> WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html > > > > I have been using gcg pretty outputs that I import into MS word as a > picture, then you can draw boxes, arrows, etc. That way seems fairly > WSYWYG, unlike trying any of the other drawing programs. It is however, > fairly crude. Good luck, > > Claudia Sutton > aka cas9@cornell.edu >> ------------------------------------------------------------------------ Actually, I am useing a lineup with no boxes, then I import the sequence into Mac MacDrawPro ( print setting set to "precise text" in preferences). when you use Courier 10, or Courier 12, the characters match exactly on the inch, i.e. 10 gives 12 characters per inch, size 12 gives 10 characters per inch. Then you set the grid to 24 divisions, and nudge the letters to conincide with the grid. Then you turn on the grid, and the boxes will now neatly snap between the letters (at half letter distances, so you have some leaway in the vertical direction, since you can't set that seperatly). Thomas Burglin From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!mcsun!EU.net!main.Germany.EU.net!fu-berlin.de!news.dfn.de!news.gwdg.de!amuelle3 From: amuelle3@gwdu19.gwdg.de (Arne Mueller ) Newsgroups: bionet.software Subject: Re: Plasmid Software:?Macplas* for PC Date: 2 Sep 1996 20:16:18 GMT Organization: GWDG, Goettingen Lines: 19 Message-ID: <50ffai$80s@gwdu19.gwdg.de> References: <1996Sep2.115456.18900@ucl.ac.uk> NNTP-Posting-Host: gwdu08-fddi.gwdg.de X-Newsreader: TIN [version 1.1 PL8] Daniel Fishman (rekadxf@ucl.ac.uk) wrote: : Is there a PC version of the Mac plasmid drawing program called something : like 'Macplasmap'? : Or otherwise does anyone know of a GOOD Windows plasmid mapping program : preferably with up to date restriction sites and good OLE function. : Thanks, : Daniel. Sorry I cant' help you but I'm interested in souch a program, too, but only for linux. thanks, Arne From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!BACATA.USC.UNAL.EDU.CO!eramirez From: eramirez@BACATA.USC.UNAL.EDU.CO (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: help to find www Date: 2 Sep 1996 15:50:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am looking for the way to find a www server where tyhe give me a domain and besides rent me some space on their HD, I know there are some companyes in the State that work in this field, can some one tell me how can I contact one of them, or how can I find some one who rents em some space in a HD of a computer connected to the internet with www server avilable, and who besides can give me the domain. thanks a lot, I really need to find a solution. bye From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!cs.utexas.edu!swrinde!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!mcsun!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bcc.ac.uk!news From: Daniel Fishman Subject: Plasmid Software:?Macplas* for PC Sender: news@ucl.ac.uk (Usenet News System) Message-ID: <1996Sep2.115456.18900@ucl.ac.uk> Date: Mon, 2 Sep 1996 11:54:56 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Organization: University College London Lines: 10 Is there a PC version of the Mac plasmid drawing program called something like 'Macplasmap'? Or otherwise does anyone know of a GOOD Windows plasmid mapping program preferably with up to date restriction sites and good OLE function. Thanks, Daniel. From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!surfnet.nl!netkid.att.nl!gatekeeper.sandoz.att.nl!root From: Reinhard Doelz Newsgroups: bionet.software Subject: Re: Sequence alignment documentation Date: Mon, 02 Sep 1996 08:12:39 +0200 Organization: a Digital Internet AlphaServer Site Lines: 26 Message-ID: <322A7AD7.41C6@GWA.SANDOZ.COM> References: <2016.9608152141@dse> <32142189.A7B@bbsrc.ac.uk> <1996Sep2.024526.46831@yogi.urz.unibas.ch> NNTP-Posting-Host: bigone.chbs.sandoz.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP19) CC: o.gallay@ic.ac.uk burglin@ubaclu.unibas.ch wrote: > > wrote: > >> o.gallay@ic.ac.uk wrote: > >> > Does anyone out there know of a program that will draw a frame around > >> > homologous segments of sequence in alignments, ie. like "prettybox" but > >> > without the shading? I've often seen this sort of frame in ... > > I have been using gcg pretty outputs that I import into MS word as a > > picture, then you can draw boxes, arrows, etc. That way seems fairly > > WSYWYG, unlike trying any of the other drawing programs. It is however, > > fairly crude. Good luck, ... > then I import the sequence into Mac MacDrawPro ( > print setting set to "precise text" in preferences). > when you use Courier 10, or Courier 12, the ... The "prettyplot" program which is a 'pretty' derivative with precisely the graphics output that is needed. This program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK) and is part of the 'EGCG package' which is available freely to all who run a valid GCG environment. Regards Reinhard From owner-software@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!nntp04.primenet.com!nntp.primenet.com!news.asu.edu!usenet From: "A. Spanias" Newsgroups: bionet.software Subject: Short Courses Date: Mon, 02 Sep 1996 12:49:52 -0700 Organization: Arizona State University Lines: 42 Message-ID: <322B3A60.17F0@asu.edu> NNTP-Posting-Host: enpc789.eas.asu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) * Announcing Two Short Courses in Image Processing & Voice Recognition * ** September 1996 in Phoenix Arizona ** (1) Fundamentals of Voice Recognition September 23-24, 1996 (2 days) Instructors: Prof. Andreas Spanias & Dr. Philip Loizou of Arizona State University Includes: Priciples and Applications Description of Algorithms and Applications (2) Image Processing September 25-27, 1996 (3 days) Instructor Prof. Tas Venetsanopoulos of University of Toronto Includes Fundamentals and Applications Description of Compression Standards At Wyndham Garden Hotel, Chandler (Phoenix), Arizona Coordinator for both courses: Andreas Spanias of Arizona State University **** Group and Early registration Discounts *** If you need a complete brochure Send email to: spanias@asu.edu Please include: name company (include mail stop) address city, state, zip phone/fax email From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Hyunsu Bae Newsgroups: bionet.software Subject: Re: Plasmid Software:?Macplas* for PC Date: Mon, 02 Sep 1996 21:22:45 -0500 Organization: UIC Lines: 22 Message-ID: <322B9675.37F1@uic.edu> References: <1996Sep2.115456.18900@ucl.ac.uk> <50ffai$80s@gwdu19.gwdg.de> NNTP-Posting-Host: e003a.phyb.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Arne, try DNAStar. It works fine for me. Arne Mueller wrote: > > Daniel Fishman (rekadxf@ucl.ac.uk) wrote: > : Is there a PC version of the Mac plasmid drawing program called something > : like 'Macplasmap'? > > : Or otherwise does anyone know of a GOOD Windows plasmid mapping program > : preferably with up to date restriction sites and good OLE function. > > : Thanks, > > : Daniel. > > Sorry I cant' help you but I'm interested in souch a program, too, but only for > linux. > > thanks, > > Arne From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!news.nap.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!chaos.crhc.uiuc.edu!news2.acs.oakland.edu!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: GeneDoc address Date: Tue, 03 Sep 1996 18:26:21 GMT Organization: Concentric Internet Services Lines: 26 Message-ID: <50hteb$rio@herald.concentric.net> References: NNTP-Posting-Host: cnc500178.concentric.net X-Newsreader: Forte Free Agent 1.0.82 GeneDoc's URL is http://www.cris.com/~ketchup/genedoc.shtml Also, most web search engines will kick up a few references to GeneDoc's home page. Thanks for you interest. Karl Nicholas. >Hello All, > I recently upgraded from one computer to another and I would like >to get the latest version of GeneDoc, which does a very nice job of >preparing output from multiple sequence alignements. I no longer have the >URL handy, and was hoping someone out there could post the location. > Thanks, > Marc Goldstein > magoldst@ix.netcom.com From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.fundp.ac.be!newsmaster From: baudou@lysine.biq.fundp.ac.be (Guy Baudoux) Newsgroups: bionet.software Subject: new multiple sequences alignment server Date: 3 Sep 1996 16:03:43 GMT Organization: FUNDP, Namur, Belgium Lines: 205 Sender: -Not-Authenticated-[7278] Message-ID: <50hksv$9v6@hermes.fundp.ac.be> NNTP-Posting-Host: biq-mac1.biq.fundp.ac.be X-Posted-From: InterNews 1.0.7@biq-mac1.biq.fundp.ac.be Xdisclaimer: No attempt was made to authenticate the sender's name. MM MM BBBBBBB MMM MMM BB B MM M M MM AA TTTTTT CCCC HH HH BB B OOOOO XX X MM M M MM AAAA TT CC HH HH == BBBBBBB OO OO XX X MM M M MM AA AA TT CC HHHHHHH == BB B OO OO XX MM M M MM AAAAAAAA TT CC HH HH BB B OO OO X XX MM M MM AA AA TT CCCC HH HH BBBBBBB OOOOO X XX Match-Box Server 1.1 multiple sequence alignment server. Guy Baudoux, Isabelle Reginster, Pascal Briffeuil, Eric Depiereux and Ernest Feytmans. Laboratory of Structural Molecular Biology, University of Namur, Belgium Rue de Bruxelles, 61 : Tel: +32-81-72-44-15 5000 Namur, Belgium : Fax: +32-81-72-44-15 E-mail: matchbox-help@biq.fundp.ac.be Project supported by the Walloon Government, Federal State of Belgium. PRESENTATION: We are pleased to announce the availability of a new sequence alignment server, based on the Match-Box software developped by Drs. Eric Depiereux and Ernest Feytmans (1,2). The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement: in the Match-Box method the gaps are the result of the alignment and not a governing parameter of the matching procedure. The method produces reliable results, as assessed by the tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation with a threshold of similarity progressively raised to extend the aligned regions to their maximal length. The score obtained at each position of the final alignment is printed below the sequences and allows a discriminant reading of each aligned region. Several additional outputs present pairwise similarity analyses in order to allow delineation of relevant subsets of related sequences and to avoid alignment of unrelated sequences. EXAMPLE: The lysozyme and alpha-lactalbumin is a well-known family of enzymes discussed in depth by H.A.McKenzie and F.H.White (3). The sequences of the lysozymes structures 1ALC, 1LZ1, 2LZ2 and 2LZT were aligned with the Match-Box server that gives the following result: Sequences number, length and name _________________________________ 1 122 1ALC 2 130 1LZ1 3 129 2LZ2 4 129 2LZT 10 20 30 40 50 60 70 + + + + + + + 1 kqftkcelsqnlyd--idgygrialpelictMFhtsgydtqai--vendesteyglfqisnalwckssqs 2 kvfercelartlkrLGmdgyrgislanwmclAKwesgyntratNYnagdrstdygifqinsrywcndgkt 3 kvygrcelaaamkrLGldnyrgyslgnwvcaAKfesnfnthatN-rntdgstdygilqinsrwwcndgrt 4 kvfgrcelaaamkrHGldnyrgyslgnwvcaAKfesnfntqatN-rntdgstdygilqinsrwwcndgrt 11111111111113 333333333444444 2222222222 1111111111111111111111111 80 90 100 110 120 130 140 + + + + + + + 1 pqsrnicditcdkflddditddimcakkild-ikgidywiahkalctEKLEQWLCEK--- 2 pgavnachlscsallqdniadavacakrvvrDpqgirawvawrnrcqNRDVRQYVQGCGV 3 pgsknlcnipcsallssditasvncakkiasGgngmnawvawrnrckGTDVHAWIRGCRL 4 pgsrnlcnipcsallssditasvncakkivsDgngmnawvawrnrckGTDVQAWIRGCRL 1111111111111111111111111111111 111111111111111 The Match-Box program tries to find "boxes" (segments that are similar in all sequences submitted by the user): residues included in the boxes are printed in lowercase. Residues in upper case are not aligned, and gaps are placed arbitrarily before the next box. A reliability score is written below each position in the boxes. It is related to the statistical significance of the alignment at this position: the lowest scores corresponds to the highest reliability of the alignment. ACCESSIBILITY: The Match-Box server is available at the Web site: http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html Using this web page, you can submit up to 50 protein sequences of no more than 2000 amino-acids each and receive by e-mail 2 output listings, resulting from two different analysis: * explore : analyses the global similarities between the sequences. * align : produces boxes (blocks) detected in the sequences and arranged in the form of a multiple alignment. This server can also be reached by electronic mail at the address: matchbox@biq.fundp.ac.be where you can send the key word "help" in the body of the message to receive informations about the methods of e-mail submission of data. In a preliminary test period, the server is accessible to any person from academic or commercial institutions. A version of the software, as a standalone program with a graphic interface is under developement. INPUT: The sequences can be submitted in FASTA-like, HSSP, or MSF formats, and the scoring matrices used by the programs can be selected directly from the web page. OUTPUT: The Match-Box server returns by default two listings "explore" and "align". Moreover the user can also ask to receive an alignment in MSF or HSSP format, and a picture of the alignment in PostScript format. DOCUMENTATION: The web page gives access to a series of documents: general presentation, details about the method, examples with explanation of the results. REFERENCES: 1. Depiereux, E. & Feytmans, E. (1991). Simultaneous amd multivariate alignment of protein sequences: correspondance between physicochemical profiles and structurally conserved regions (SCR). Prot. Engng. 4(6), 603-613. 2. Depiereux, E. & Feytmans, E. (1992). MATCH-BOX - A fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Appl. Biosci. 8(5), 501-509. 3. McKenzie, H.A. & White, F.H. (Jr) (1991). Lysozyme and alpha-lactalbumin, function and interrelationships. Adv. Prot. Chem. 41, 173-258. From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!brighton.openmarket.com!wizard.pn.com!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software Subject: What else you can do with a protein sequence Date: 3 Sep 1996 13:24:59 GMT Organization: EMBL Heidelberg Lines: 19 Distribution: world Message-ID: <50hbjb$ror@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software What else you can do with a protein sequence .... 1 find composition 2 calculate mol weight .... 3 . . Let us see the growth of this list... =============================================================== Ramu C | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg Fax: (49) 6221 387517 | Germany http://www.embl-heidelberg.de/~chenna/ ------------------------------------------------------------- From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.primenet.com!news.primenet.com!not-for-mail From: Jonathan Teets Newsgroups: bionet.software Subject: A/D cards Date: 3 Sep 1996 09:05:02 -0700 Organization: Noraxon USA, Inc. Lines: 17 Message-ID: <322C54CA.26F8@noraxon.com> X-Posted-By: @198.68.46.98 (fermigas) X-Mailer: Mozilla 2.01Gold (WinNT; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Analog to Digital converter cards for sale. All lightly used, all popular models from Data Translation: 1 DT2839: 32 chanels, 12 bit, 1Mhz, $1700 (retails for ~$3000.00) 4 DT2821: 16 channels, 12 bit, 150Khz, $950 (retail ~$2000.00) 6 DT2801A: 16 channels, 12 bit, 27Khz, $550 (retail ~$1000.00) I also have software for the cards. Jon Teets Phoenix, AZ jteets@noraxon.com From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!info.ucla.edu!csulb.edu!news.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!bentley!deleage From: deleage@bentley (deleage@ibcp.fr) Newsgroups: bionet.software Subject: Antheprot Date: 3 Sep 1996 11:18:13 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Lines: 17 Message-ID: <50h45l$o4b@cri.ens-lyon.fr> NNTP-Posting-Host: ibcp.fr X-Newsreader: TIN [version 1.2 PL1] Doug, You didn't tell which kinds of print? (Text print, graphic printings) What is your configuration (CPU, printer, RAM size)? Note that I am developping ANTHEPROT onto a COMPAQ DX250 contura 410 C running Win95 with 8Mb RAM coupled to either a Lexmark 4079 or HP550C. Is the printing subsystem telling you anything? SY, Gilbert -- ===================================================================== # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # # ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # # # 7, passage du Vercors # # # ***** # # # 69367 Lyon Cedex 07,FRANCE # # # # # # #**** Tel: (33) 72-72-26-47 # # # # # # # # Fax: (33) 72-72-26-01 # # ***** ****** **** # deleage@ibcp.fr # ===================================================================== From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: help to find www Date: 3 Sep 1996 04:42:07 GMT Organization: Best Internet Communications Lines: 12 Distribution: world Message-ID: <50gcuv$gdh@nntp1.best.com> References: NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] EFRAIN RAMIREZ ZAPATA (eramirez@BACATA.USC.UNAL.EDU.CO) wrote: : I am looking for the way to find a www server where tyhe give me a domain : and besides rent me some space on their HD, I know there are some : companyes in the State that work in this field, can some one tell me how : can I contact one of them, or how can I find some one who rents em some : space in a HD of a computer connected to the internet with www server : avilable, and who besides can give me the domain. thanks a lot, I really : need to find a solution. bye Not strictly a Biosoftware issue, but several companies here do this for around about $20/month. (eg. try http://www.best.com, http://www.digiweb.com etc. etc. etc.) From owner-software@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!btnet!netcom.net.uk!ix.netcom.com!news.compuserve.com!news.production.compuserve.com!news From: Mark Miller <70176.1153@CompuServe.COM> Newsgroups: bionet.software Subject: New Australian REPTILE CDROM available. Date: 3 Sep 1996 10:33:30 GMT Organization: Herp-Net 215-464-3562 BBS Lines: 37 Message-ID: <50h1hq$fhj$14@mhafn.production.compuserve.com> NEWS RELEASE: For Immediate release ANNOUNCING AUSTRALIA'S REPTILES -- CD-ROM VERSION II This exciting new CD-ROM contains more than 900 COLOR PHOTOGRAPHS of Australia's terrestrial reptiles: venomous and nonvenomous snakes, monitors (goannas), dragons, geckos, and other lizards. It contains the full text of Wilson & Knowles out-of-print book with updated material. Reptile species can be selected by scientific name, common name, genus, or family. Each species record contains notes on description, biology, conservation status, distribution, etc. The CD-ROM also contains a reptile trivia quiz, a glossary of reptile terms, and notes on the treatment of snakebite in Australia. Fascinating video clips are included from many of the Australian reptile parks. The CD-ROM is designed for herpetologists, schools, libraries, naturalists, herp societies, and reptile enthusiasts with an MPC standard IBM-type multimedia computer with CD-ROM drive and sound. We regret that no Macintosh version is available at this time. Version II contains BOTH Vol. 1 and 2 in this series on one CD-ROM. (These were issued at $49 each in the past.) Australia's Reptiles, Version II is available for US$49 plus $3 shipping ($5 outside North America) from Satronics Communications, PO Box 52261, Philadelphia PA 19115-7261 USA. Check or M.O. in US$. For additional information,questions or support please email: 70176.1153@compuserve.com or fax 215-464-3561 anytime. ### From owner-software@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!abreu From: abreu@SERVIDOR.DGSCA.UNAM.MX ("F. Alberto Abreu Grobois") Newsgroups: bionet.software Subject: GENETIC ANALYSIS PROGRAMS Date: 4 Sep 1996 11:10:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <1.5.4.32.19960904181153.0066e2c0@servidor.unam.mx> NNTP-Posting-Host: net.bio.net Dear netters: Could someone be able to tell me where I can obtain copies of the following computer programs, ideally in a PC-compatible format? AMOVA (Excoffier et al., 1992) HAPLO (Lynch & Crease, 1990) UPGMAL ( " ) Thank you very much, Alberto Abreu From owner-software@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!mcsun!EU.net!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!ddsw1!news.mcs.net!van-bc!news.mindlink.net!news.atl.bellsouth.net!newsrelay.iastate.edu!news.iastate.edu!news From: An-Ping Hsia Newsgroups: bionet.software Subject: FileMaker3.0 Date: Wed, 04 Sep 1996 15:39:15 -0500 Organization: Iowa State University Lines: 7 Message-ID: <322DE8F3.7483@iastate.edu> NNTP-Posting-Host: mac20197.agron.iastate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Hi, I am trying to set up a database for our lab. It will contain information about clones, vectors and purchasing record. I am using Excel now. I would like to know if anybody compared FileMaker3.0 and Excel or any comment about FileMaker3.0. Thanks in advance. From owner-software@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!mawny.microagewny.com!usenet From: dpeaston@microagewny.com (Doug Easton) Newsgroups: bionet.software Subject: Re: Antheprot Date: Wed, 04 Sep 1996 00:36:47 GMT Organization: MicroAge of Western New York Lines: 29 Message-ID: <50ig44$qd7@mawny.microagewny.com> References: <50h45l$o4b@cri.ens-lyon.fr> NNTP-Posting-Host: ppp0.microagewny.com X-Newsreader: Forte Free Agent 1.0.82 deleage@bentley (deleage@ibcp.fr) wrote: >Doug, >You didn't tell which kinds of print? (Text print, graphic printings) >What is your configuration (CPU, printer, RAM size)? >Note that I am developping ANTHEPROT onto a COMPAQ DX250 contura 410 C >running Win95 with 8Mb RAM coupled to either a Lexmark 4079 or HP550C. >Is the printing subsystem telling you anything? >SY, Gilbert >-- > ===================================================================== > # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # > # ***** ***** **** ***** Dr Gilbert Deleage # > # # # # # # # # 7, passage du Vercors # > # # ***** # # # 69367 Lyon Cedex 07,FRANCE # > # # # # # #**** Tel: (33) 72-72-26-47 # > # # # # # # # Fax: (33) 72-72-26-01 # > # ***** ****** **** # deleage@ibcp.fr # > ===================================================================== Sorry, Problem mostly my fault. I was too impatient and began clicking on things before the print began. On my system it is extreemley slow in spooling the graphics printing (3-4 minutes) for a page. The clicking on things like the close button will eventually freeze the machine. -Doug Easton From owner-software@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!mcsun!EU.net!main.Germany.EU.net!fu-berlin.de!cs.tu-berlin.de!informatik.uni-bremen.de!gina.zfn.uni-bremen.de!wdmeyer From: wdmeyer@fbm.hs-bremen.de (Peter Wedemeyer) Newsgroups: bionet.software Subject: AL software for mac Date: Wed, 04 Sep 1996 13:36:35 +0200 Organization: Hochschule Bremen Lines: 6 Message-ID: NNTP-Posting-Host: mlbf05.fbm.hs-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 Hello Evererybody! Does anyone know anything about an ARTIFICIAL LIFE prog. for the mac (like tierra)? e-mail:wdmeyer@fbm.rz.hs-bremen.de From owner-software@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!ARTSCI.WUSTL.EDU!mpion From: mpion@ARTSCI.WUSTL.EDU (Martin Pion) Newsgroups: bionet.software Subject: Re: FileMaker3.0 Date: 4 Sep 1996 15:43:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi An-Ping, I was going literally out of my mind trying to get by with Excel when first establishing a home-based office until a friend introduced me to FileMaker. It's absolutely essential for all my database needs now, e.g. mail lists, orders, requests, you name it. Regards, Martin. At 3:39 PM 9/4/96, An-Ping Hsia wrote: >Hi, >I am trying to set up a database for our lab. It will >contain information about clones, vectors and >purchasing record. I am using Excel now. I would >like to know if anybody compared FileMaker3.0 and >Excel or any comment about FileMaker3.0. Thanks in >advance. From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Iosif Vaisman Newsgroups: bionet.general,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.molbio.methds-reagnts,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.cellbiol,bionet.jobs,bionet.software.gcg,bionet.molbio.bio-matrix Subject: Computational Molecular Biology Workshop, October 15-19, 1996 Date: 5 Sep 1996 15:03:54 -0700 Organization: The University of North Carolina at Chapel Hill Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23165 bionet.biophysics:2276 bionet.molbio.proteins:8677 bionet.molec-model:1132 bionet.molbio.methds-reagnts:48854 bionet.software:16470 bionet.structural-nmr:1480 bionet.xtallography:2850 bionet.cellbiol:5405 bionet.software.gcg:1978 bionet.molbio.bio-matrix:755 CAROLINA WORKSHOPS University of North Carolina at Chapel Hill Computational Molecular Biology October 15 - 19, 1996 This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1996. Tuition - $ 1,200.00. Participation is limited to 15 people. COURSE DIRECTOR: Alexander Tropsha, Ph.D., University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Oxford Molecular) David C. Richardson (Duke University) Wayne Litaker (UNC-Chapel Hill) Alexander Tropsha (UNC-Chapel Hill) Michael Mitchell (UNC-Chapel Hill) Iosif I. Vaisman (UNC-Chapel Hill) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 442 Taylor Hall CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 E-MAIL litaker@med.unc.edu From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!cs.utexas.edu!swrinde!cssun.mathcs.emory.edu!news.service.emory.edu!news From: timmer@physio.emory.edu Newsgroups: bionet.software Subject: Re: FileMaker3.0 Date: Thu, 05 Sep 96 09:26:24 PDT Organization: Emory University Lines: 21 Message-ID: References: <322DE8F3.7483@iastate.edu> NNTP-Posting-Host: gunnlab2.physio.emory.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage In Article<322DE8F3.7483@iastate.edu>, writes: > Hi, > I am trying to set up a database for our lab. It will > contain information about clones, vectors and > purchasing record. I am using Excel now. I would > like to know if anybody compared FileMaker3.0 and > Excel or any comment about FileMaker3.0. Thanks in > advance. I've been using Filemaker Pro for this and several other lab type databases, and I find that it works great. The database was easy to set up, and the final user interface/forms are easy for other less-computer oriented lab colleagues to use. I found Excel would work, but required more effort on my part to design something that was accessible for others to easily and willingly use. Just my $0.02. Cheers, Richard Timmer From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.software Subject: Biomx, electronic journal in English or Spanish Date: 5 Sep 1996 12:57:23 -0700 Organization: UANL Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <322F4D46.7D71@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net I would much appreciate receiving a review of biosoftware. Please see the homepage for more: Under Yahoo search, enter BIOMX. or http://www.uanl.mx/biomx Thank you, Dr Paul R Earl From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!psgrain!nntp.teleport.com!usenet From: jdobson@rnib.org.uk (James Dobson) Newsgroups: bionet.software Subject: Is there a links in links out piece of software for a www site Date: Thu, 05 Sep 1996 10:03:40 GMT Organization: Royal National Institute for the Blind Lines: 8 Message-ID: <50m8fg$go9@nadine.teleport.com> NNTP-Posting-Host: host-16-232.rnib.org.uk X-Newsreader: Forte Free Agent 1.0.82 I'm look for a windows (3.1) software that is able to produce a graphical or a html report on the structure of a site in particular the links in and links out of particular files. I know of Web Anayzer and its HTML reports are rubbish, taking ages to load them up. If you know of a piece of software or even better a downloadable piece of software PLEASE tell me!!! Thanks. From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!demos!news.florin.ru!office!kps From: kps@office (Konstantin P. Savov) Newsgroups: bionet.software,bionet.plants,sci.bio.botany,sci.bio.misc,sci.bio.systematics Subject: FLORIN Home Page Date: 5 Sep 1996 19:55:31 GMT Organization: DataX/FLORIN, Inc. Lines: 27 Message-ID: <50nb7j$iak@nic.florin.ru> NNTP-Posting-Host: office.florin.ru X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:16469 bionet.plants:12437 sci.bio.botany:2802 sci.bio.misc:4719 sci.bio.systematics:1148 FLORIN Information System Home Page is available on http://www.florin.ru/florin/ FLORIN is an information system designed to deal with a wide range of data about plants: taxonomy and nomenclature, geographic distribution, herbarium and living collections, detailed information about plants collected in the wild, bibliographic data, etc. Personal MS-DOS and multiuser Unix versions are available. The System supprots data entry and modification, query-by-example templates, configurable reports, data browsing, loading and importing data, GIS interface for geographic data, automated generation of labels for collections, collection management, data protection and authorization, Internet access, etc. You are welcome! -- +---------------------------------------------------------------------------+ | Konstantin Savov | DataX/FLORIN, Inc. Moscow, Russia | | | Advanced Data Management Systems | | E-mail: kps@florin.ru | Voice: (095)158-9520 Fax: (095)158-5700 | +---------------------------------------------------------------------------+ FLORIN Home Page: "http://www.florin.ru/florin/" From owner-software@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Peter Kulmburg Newsgroups: bionet.software Subject: mac printer driver for HP LaserJet 4si? Date: 5 Sep 1996 13:21:51 +0100 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50mgkv$djr@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Dear collegues, I am one of the rare Mac users in a Novell net made up by PCs. We have a net printer HP LaserJet 4si and I would like to print on it. Using the novell net client 5.1 for Mac, I can send print batches to the print queue but nothing comes out the printer. Since I am using the driver originally designed for the HP LaserJet 4 ML, it might be a problem with this driver. Can anybody give me a hint where I can find the driver for the 4si for novell nets? Thank you very much in advance! Sincerely yours 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 Wed Sep 04 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!uchinews!uwvax!newssinet!ehime-u!surg2_171.m.ehime-u.ac.jp!user From: yasuhito@m.ehime-u.ac.jp (Yasuhito Abe) Newsgroups: bionet.software Subject: DNA programs for Windows Date: Fri, 06 Sep 1996 07:40:52 +0900 Organization: 2nd Dept of Surgery, Ehime Univ Lines: 14 Message-ID: NNTP-Posting-Host: surg2_171.m.ehime-u.ac.jp Dear netters, I am now launching my molecular work using a newly introduced Windows machine. Could somebody introduce me useful shareware sites for DNA analysis, such as alignment and primer design, using Windows(95)? Thank you for your cooperation. Yasuhito Abe The Second Deparment of Surgery, Ehime University School of Medicine Shigenobu, Ehime 791-02 Japan e-mail: yasuhito@m.ehime-u.ac.jp www: http://www.m.ehime-u.ac.jp/~yasuhito/Home.html From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.software Subject: ANNOUNCE ProAnalyst -- new software for protein/peptide analysis Date: 6 Sep 1996 11:21:00 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 102 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50otuc$9gi@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk To: bio-software@dl.ac.uk From: eroshkin@vector.nsk.su Subject:ANNOUNCE ProAnalyst - new software for protein/peptide analysis ------------------------ ProAnalyst - PROTEIN ANALYST ver 1.02 ------------------------ State Research Center of Virology and Biotechnology Koltsovo, Novosibirsk Region, 633159 Russia and Vladimir Ivanisenko with Alexey Eroshkin are pleased to announce the availability of an easy-to-use, state-of-the-art MS-DOS application designed to solve traditional and new tasks of protein science. ProAnalyst FEATURES: - inputs single and multiple protein sequences, activity/property/ genotype data, protein 3D structures; - finds sites influencing protein activity; - finds relationships between protein sites' structural characteristics (hydrophobicity, amphipathicity, etc.) and protein activities; - investigates differences between proteins divided by functional, evolutionary or other criteria (e.g. relates genotype to phenotype); - investigates physico-chemical factors related with activity changes in a set of mutant proteins (including multiple physico-chemical factors); - simulates protein-engineering experiments and predicts activity of mutant protein; - searches motifs and patterns in combinatorial libraries (peptide and phage-displayed libraries); - makes protein stereo pictures with sites highlighted; - provides linear correlation analysis, multiple linear regression analysis, discriminant analysis, ANOVA (analysis of variance), alphabetical and classic profile/plot analysis; - searches regions with high and low variability of physico-chemical characteristics; - calculates structure-activity correlation profile; - performs cross and inter-group variability analysis based on several matrices of amino acid similarity; - main part of methods are applicable to sequential as well as 3D sites; - maps obtained results onto 3D structure; - sorts sequences by activty, group number, motifs found; - visualizes multiple alignments and protein 3D structures (stereo); - has data converter from several protein sequence formats (FASTA, SWISS-PROT, CLUSTAL, PIR, IG); - has data bases with 50 aligned protein families, more then 60 amino acid properties, HELP, Manual and examples with program applications. ProAnalyst MAY BE USEFUL: - for chemists and biochemists making the investigations in the field of protein structure-function and structure-activity analysis; - for protein engineers trying to improve some protein properties; - for molecular biologists that need to get sense from multiple protein alignments and to analyze complicated combinatorial libraries; - for geneticists studying phenotype-genotype correlations; - for those who need color protein 3D pictures with sites highlighted; - for students in any field of PROTEIN SCIENCE; - for those who interested in comparative protein sequence analysis. AVAILABILITY: ProAnalyst is available from EBI software library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/ (as self-extracted archive). Current version works with up to 15 sequences. The length of sequences must be less than or equal to 5000. Comments, bug reports, suggestions for new features are welcome and should be sent by e-mail to: salex@vector.nsk.su (Vladimir Ivanisenko) or eroshkin@vector.nsk.su (Alexey Eroshkin) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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 Thu Sep 05 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!chaos.kulnet.kuleuven.ac.be!usenet From: Przemko Tylzanowski Newsgroups: bionet.software Subject: Re: DNA programs for Windows Date: Fri, 06 Sep 1996 08:18:42 +0200 Organization: K.U.Leuven Lines: 35 Message-ID: <322FC242.41C6@sgi.celgen.kuleuven.ac.be> References: NNTP-Posting-Host: sgi.celgen.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5aGold (X11; I; IRIX 5.3 IP22) Yasuhito Abe wrote: > > Dear netters, > I am now launching my molecular work using a newly introduced > Windows machine. Could somebody introduce me useful > shareware sites for DNA analysis, such as alignment and > primer design, using Windows(95)? Thank you for your cooperation. snip... isn't it funny that periodically someone asks, BEGS, for decent share/freeware programs for windows. Programs that would: - draw simple plasmid maps - helps in drawing restriction maps from restriction data (gels) - allows some other, simple data manipulation, such as editing of sequences, saving them in a few commonly used formats (why the hell there are so many of them beats me...) etc. Now, there are a few programs available but: - anything for plasmid drawing, restriction map making is $$$$$$ - the is NO PROGRAM (as far as my net searches go)for Win95 that would take data from single and multiple restriction digests and assemble it into a restriction map. The only program that I know of that would do that is included into IG Suite package (Sun or VAX?). And another program that goes in that direction is DoubleDigester (forgot the author- sorry) but even that will do only two enzymes. - there is Sequp but that very efficiently crashes my machine (Pentium 100, 1Gb hard drive, 32Mb RAM). There was an old version of that program for DOS, alas, DOS is dead... So, it seems that if I would have bought a Mac then I could have all I want. Is it so difficult to write something for Win95, or simply the educational strategy of Apple caused that once hooked to it in college dorm, one just stays with it... Przemko From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!MBOX.STETSON.EDU!barkalow From: barkalow@MBOX.STETSON.EDU (Derek Barkalow) Newsgroups: bionet.software Subject: Lab View Virtual Bench opinions? Date: 6 Sep 1996 05:04:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <32301392.633B@mbox.stetson.edu> Reply-To: @worldnet.att.net NNTP-Posting-Host: net.bio.net Would appreciate assistance in finding users of this software in the undergraduate lab setting. We are setting up a new neurobiology lab and wonder about the ease of use of Virtual Bench for undergrads? Our primary goal is to use this SW to replace traditional oscilloscopes. Are other software data acquisition and processing systems available with particular applicability to neurobiology? Thanks in advance. Mike King Biology Dept. Stetson University mking@mbox.stetson.edu From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!tty24.maze.ppp.uab.edu!user From: biof020@uabdpo.dpo.uab.edu (Debbie Moore) Newsgroups: bionet.software Subject: net software for Mac Powerbook 5300 Date: Fri, 06 Sep 1996 17:53:44 +0000 Organization: University of Alabama at Birmingham Lines: 6 Message-ID: NNTP-Posting-Host: tty24.maze.ppp.uab.edu Could someone recommend software for the 5300cs Mac Powerbook for net access, etc.? As a student I am limited in funds, but would like the flexibility of taking the net and email with me when I travel. Thanks for any help. DMoore@uab.edu From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!main.Germany.EU.net!fu-berlin.de!news.th-darmstadt.de!News.Uni-Marburg.DE!usenet From: becker@ps1515.chemie.uni-marburg.de (Andreas Becker) Newsgroups: bionet.software Subject: Re: DNA programs for Windows Date: Fri, 06 Sep 1996 21:45:31 GMT Organization: Universitat, 35039Marburg, Germany Lines: 25 Message-ID: <50q65h$lph@surz03fi.HRZ.Uni-Marburg.DE> References: Reply-To: becker@ps1515.chemie.uni-marburg.de NNTP-Posting-Host: nnex01.ppp.uni-marburg.de X-Newsreader: Forte Free Agent 1.0.82 yasuhito@m.ehime-u.ac.jp (Yasuhito Abe) wrote: >Dear netters, >I am now launching my molecular work using a newly introduced >Windows machine. Could somebody introduce me useful >shareware sites for DNA analysis, such as alignment and >primer design, Take a look at my home page >using Windows(95)? Thank you for your cooperation. Why should anyone support this??? Andreas Becker ---------------------------------------------------------------------- Andreas Becker Arbeitskreis Prof. Kadenbach, FB Chemie/Biochemie, Hans- Meerwein-Strasse, Philipps-Universitaet, 35043 Marburg, Germany Phone: privat +49 6421 47304 Labor +49 6421 28 -5721 Fax -2191 eMail: BECKER@ps1515.Chemie.Uni-Marburg.De WWW : http://www.chemie.uni-marburg.de/~becker From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!chaos.crhc.uiuc.edu!news2.acs.oakland.edu!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: Q:Sequence Alignemnt on Win-PC? Date: Fri, 06 Sep 1996 17:49:12 GMT Organization: Concentric Internet Services Lines: 21 Message-ID: <50pocp$7k3@herald.concentric.net> References: NNTP-Posting-Host: cnc146036.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Have a look a GeneDoc. It wont create an alignment program for you, clustalw can do that, but you can then edit, shade and annotate the alignment. http://www.cris.com/~Ketchup/genedoc.shtml >Hello, >I was wondering if anybody knows a nice sequence alignmment >program that runs on a PC? >Thanks for your help! >Cheers, > Agustin From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!GREEN.DFCI.HARVARD.EDU!agustin From: agustin@GREEN.DFCI.HARVARD.EDU (Agustin de la Calle) Newsgroups: bionet.software Subject: Q:Sequence Alignemnt on Win-PC? Date: 6 Sep 1996 07:28:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Agustin de la Calle NNTP-Posting-Host: net.bio.net Hello, I was wondering if anybody knows a nice sequence alignmment program that runs on a PC? Thanks for your help! Cheers, Agustin From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!BCBP.GU.SE!anders From: anders@BCBP.GU.SE (Anders Bergkvist) Newsgroups: bionet.software Subject: C++ class library (NMR matrix conversions)... Date: 6 Sep 1996 06:16:18 -0700 Organization: Dept. of biochemistry and biophysics, Göteborg, Sweden Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <3230A304.6F25@bcbp.gu.se> NNTP-Posting-Host: net.bio.net Hi netters! I am a PhD student in biophysics with the main interest in structure determination with NMR. Recently I've had some desire to make my own computer programs for manipulation of NMR spectrum matrices. Is there anyone who has a C++ class library for i/o from/to different matrix formats (e.g. Varian, Bruker, Felix, etc...)? Other information about matrix format would also be useful for me or other computer language codes, like fortran, etc, for this purpose. Thanks, Anders Bergkvist Dept. of biochemistry and biophysics Göteborgs University Sweden anders@bcbp.gu.se From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news.sgi.com!esiee.fr!jussieu.fr!news.edf.fr!newsadm From: "Jean-Baptiste Briaud (Stagiaire)" Newsgroups: bionet.software Subject: Re: DNA programs for Windows Date: Fri, 06 Sep 1996 14:46:50 +0200 Organization: E.D.F. Lines: 17 Message-ID: <32301D3A.375C@cli29aa.der.edf.fr> NNTP-Posting-Host: cli29at.der.edf.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) : Yasuhito Abe wrote: : > I am now launching my molecular work using a newly introduced : > Windows machine. Could somebody introduce me useful : > shareware sites for DNA analysis, such as alignment and : > primer design, using Windows(95)? Thank you for your cooperation. : snip... : : isn't it funny that periodically someone asks, BEGS, for decent : share/freeware programs for windows. Programs that would: :[...] : Przemko I'm afraid it is due to the lack of software engeneer able to anderstand and programm biological problems. Is biologist ready to begin a software developpement like an industrial projet ? With software toolcase ? From owner-software@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news From: Darren Platt Newsgroups: bionet.software Subject: Announcing Image version 3 Date: Fri, 06 Sep 1996 11:03:51 +0100 Organization: The Sanger Centre Lines: 23 Message-ID: <322FF707.59E2@sanger.ac.uk> NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6Gold (X11; I; OSF1 V3.0 alpha) We would like to announce "Image 3.2", a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments that have been tightly integrated with a friendly user interface to provide a robust tool for large scale physical mapping. Image 3.2 is able to process gels from a wide variety of scanning technologies and has been tested on various fingerprinting protocols, producing normalized bands and normalized gel images as output. The output is compatible with previous releases of Image, and is designed to work in conjunction with the mapping packages FPC or ContigC. Binaries for SunOS, Solaris, OSF/1, and Irix are currently available. Further details are available from: http://www.sanger.ac.uk/fingerprinting/imageprocessing This site includes facilities for downloading the software, reporting problems, and extensive documentation including a complete tutorial. -- Darren Platt daz@sanger.ac.uk From owner-software@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!newsfeeder.servtech.com!murphy2.servtech.com!news From: Kim Pruitt Newsgroups: bionet.software Subject: Re: FileMaker3.0 Date: Sat, 07 Sep 1996 17:26:24 -0700 Organization: Salt City Software Lines: 22 Message-ID: <323212B0.3674@cyber2.servtech.com> References: <322DE8F3.7483@iastate.edu> NNTP-Posting-Host: saltcitysw.syr.servtech.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) To: An-Ping Hsia An-Ping Hsia wrote: > > Hi, > I am trying to set up a database for our lab. It will > contain information about clones, vectors and > purchasing record. I am using Excel now. I would > like to know if anybody compared FileMaker3.0 and > Excel or any comment about FileMaker3.0. Thanks in > advance. Hi, You might be interested in looking at our latest software (Plasmid Tracker) designed to keep track of bacterial stocks. It is written for the PC and has the advantage of including a restriction map. A free demo will be released on our home page in approx. 2 weeks. http://www.servtech.com/public/saltcity Regards, Kim Pruitt Salt City Software From owner-software@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in2.uu.net!nntp.inet.fi!news.funet.fi!luotsi.uku.fi!atk03.kys.fi!usenet From: Petteri Mussalo Newsgroups: bionet.software Subject: DATA TRANSLATION DT2821 Date: Fri, 06 Sep 1996 19:11:58 -0700 Organization: Kuopio University Hospital Lines: 2 Message-ID: <3230D9EE.3D3E@kuh.fi> NNTP-Posting-Host: q4361d.kys.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Does anybody know a simple and a cheap sw to use with A/D converter 'DATA TRANSLATION DT2821' From owner-software@net.bio.net Fri Sep 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: FASTA version 3.0t7 with full PVM support available X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: wrp@alpha0.bioch.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.1 References: Date: Sat, 7 Sep 1996 16:09:15 GMT Lines: 19 Updated versions of FASTA3.0 (fasta30t7) and FASTA2.0 (fasta20u6) have been placed on ftp.virginia.edu:/pub/fasta. These versions fix another subtle problem with tfastx and fastx. In addition, fasta30t7 now contains a full-function pvm version. PVM (Parallel Virtual Machine) is a parallel progamming environment that makes it very easy to use networks of unix workstations to compute in parallel. pvcompfa and pvcompsw have been available for some time to do library vs library sequence comparisons providing scores only, but the current version also provides sequence alignments (and histograms). It uses exactly the same comparison code and statitiscal calculations as the fasta3(_t) versions. Thus, pvcompfa and pvcompsw are very well suited for performing very large scale sequence comparisons on networks of unix workstations. Bill Pearson From owner-software@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!ott.istar!istar.net!n3ott.istar!news.quebectel.com!root From: verdo68@quebectel.com (Dominique verreault) Newsgroups: bionet.software Subject: I looking for Date: 7 Sep 1996 20:05:32 GMT Organization: Globe trotter Lines: 4 Message-ID: <50skic$b8r@news.quebectel.com> NNTP-Posting-Host: ts2-07.f019.quebectel.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 I looking for Turbo Pascal for Windows 3.1, If anyone want to trade E-mail me: verdo68@quebectel.com From owner-software@net.bio.net Sat Sep 07 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!cam-news-hub1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsserver.jvnc.net!news.edu.tw!news.cc.nctu.edu.tw!suncc.ccu.edu.tw!news.nsysu.edu.tw!news From: s8313052@dec8.cyit.edu.tw (Yan-her Lin) Newsgroups: bionet.software Subject: acecad II Date: Sun, 08 Sep 1996 05:07:25 GMT Organization: National Sun Yat-san University, Taiwan Lines: 9 Message-ID: <32325467.11095492@news.nsysu.edu.tw> NNTP-Posting-Host: 140.117.10.34 X-Newsreader: Forte Agent .99e/32.227 Anyone uses the ACECAT tablet II? I want to get the ACECAD II tablet's driver. Can anyone send it to me or tell me where to get it. Thanks in advance. My Email is s8313052@dec8.cyit.edu.tw but My Emails server is downing now. So, I cannot receive any mail now. My NSYSU BBS email: alyh.bbs@bbs.nsysu.edu.tw. From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.dacom.co.kr!news.kreonet.re.kr!usenet.etri.re.kr!usenet.kornet.nm.kr!snunews.snu.ac.kr!news.kaist.ac.kr!bioneer.kaist.ac.kr!ipark From: ipark@kaist.ac.kr (Inyup Park) Newsgroups: bionet.software Subject: Data acquisition program... Date: 9 Sep 1996 14:29:51 GMT Organization: Dept. of Biological Sciences, KAIST Lines: 25 Message-ID: <5119kv$s9s@worak.kaist.ac.kr> NNTP-Posting-Host: bioneer.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] Hello bio.netters, I am currently using a Waters HPLC 486 system and "PC 800 Integrator," the bundled data acquisition program. "800" is a 2-channel, mouse-driven, and dos-based chromatography data system. The program starts up the process run immediately when the sample is injected (a Rheodyne injector). I have no problems with this program -- except for its time-limit. It automatically ends the data acquisition run at 125min. For my experiments, I need to use a very slow gradient which takes about 3 hours to complete. So, I was wondering if there are any shareware or freeware programs out there that I can use. - Doesnt't have to be fancy, but should be painless to use. :) - I don't need it to read two-channels -- one would do. - I would preferably have it scrollable. (not a must) - High-resolution of the graphic output (monitor) is desired. Well, I am crossing my fingers... InYup Park Dept. of Biological Sciences Korea Advanced Institute of Science and Technology U Penn '95 From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Newsgroups: bionet.software Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: cor@codon.nih.gov (Cor Witteveen) Subject: HP 8450 Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.99.180 Organization: LNC/NIMH Date: Mon, 9 Sep 1996 15:20:10 GMT Lines: 13 Hi, I'm using a Hewlett Packard 8450A, an old diode array spectrophotometer which is controlled by an internal Hewlett packard computer. The machine is still working fine, but analyzing my data is a drag since I am not able to get the data from the HP computer to a dos or macintosh computer. I was wondering whether anybody has a simple data aquisition program that hooks up a dos computer to the HP 8450A through the RS323 port. Controlling the machine this way is not necessary. Just data aquisition or export of stored data from the HP computer to a dos computer would be fine. please e-mail me directly: cor@codon.nih.gov thanks, Cor From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!uunet!in2.uu.net!nntp.inet.fi!news.funet.fi!news.helsinki.fi!vesuri.Helsinki.FI!not-for-mail From: stenberg@cc.Helsinki.FI (Dag Stenberg) Newsgroups: bionet.software Subject: Re: DATA TRANSLATION DT2821 Date: 9 Sep 1996 13:21:54 GMT Organization: University of Helsinki Lines: 17 Message-ID: <5115li$391@oravannahka.Helsinki.FI> References: <3230D9EE.3D3E@kuh.fi> NNTP-Posting-Host: vesuri.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [UNIX 1.3 950824BETA PLMC.960407] Petteri Mussalo wrote: > Does anybody know a simple and a cheap sw to use with > A/D converter 'DATA TRANSLATION DT2821' If you hear about one that can be used for HPLC (high pressure liquid chromatography) please mail and tell me too! ------------------------------------------------------------------ Dag Stenberg MD PhD stenberg@cc.helsinki.fi Institute of Biomedicine tel: int.+358-0-1918532 Department of Physiology fax: int.+358-0-1918681 P.O.Box 9 (Siltavuorenpenger 20 J) tlx: 1002125 finuh sf FIN-00014 University of Helsinki,Finland X.400: /C=FI/A=FUMAIL/P=INET/O=HELSINKI/OU=CC/S=STENBERG/ ------------------------------------------------------------------ From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!enews.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!surfnet.nl!swsbe6.switch.ch!swidir.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!news.informatik.uni-muenchen.de!z41.zi.biologie.uni-muenchen.de!user From: strimmer@zi.biologie.uni-muenchen.de (Korbinian Strimmer) Newsgroups: bionet.software Subject: PUZZLE version 2.5 available Date: Mon, 09 Sep 1996 14:45:01 +0200 Organization: Institute of Zoology, LMU Munich Lines: 83 Message-ID: NNTP-Posting-Host: z41.zi.biologie.uni-muenchen.de P U Z Z L E 2.5: Announcement 15 September 1996 PUZZLE is (c) 1995-96 by Korbinian Strimmer and Arndt von Haeseler Zoologisches Institut Universitaet Muenchen Luisenstrasse 14 D-80333 Muenchen Germany Voice: +49-89-5902-327 Fax: +49-89-5902-474 Email: strimmer@zi.biologie.uni-muenchen.de Email: arndt@zi.biologie.uni-muenchen.de INTRODUCTION PUZZLE is a maximum likelihood program for reconstructing phylogenetic trees from nucleotide and amino acid sequence data. It is available free of charge over the Internet and runs on all popular systems. It is distributed by the European Bioinformatics Institute: ftp://ftp.ebi.ac.uk/pub/software/dos/puzzle (DOS version) ftp://ftp.ebi.ac.uk/pub/software/mac/puzzle (MacOS version) ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle (UNIX version) ftp://ftp.ebi.ac.uk/pub/software/vms/puzzle (VMS version) PUZZLE is easy to install, easy to use, and implements a fast maximum likelihood tree search algorithm (quartet puzzling) that allows analysis of large data sets. Furthermore, this tree search automatically provides estimates of support for each internal branch. PUZZLE also computes paiwise maximum likelihood distances for all implemented models (TN, HKY, F84, and submodels; Dayhoff, JTT, mtREV). It estimates the model parameters of the HKY/TN models (ratio of transition-transversion ratio etc.) from the data. PUZZLE also estimates maximum likelihood branch lengths for the quartet puzzling tree or a specifed user tree (both for completely resolved and for multifurcating trees). SUPPORTED FEATURES Features include ($ marks features added in version 2.5): * user menu PHYLIP "look and feel" * analysis of both nucleotide and amino acid sequences * wide range of models of sequence evolution - nucleotides: Tamura-Nei 1993 Hasegawa et al. 1985 Felsenstein 1984 (PHYLIP DNAML model) $ and derivatives - amino acids: Dayhoff 1978 Jones et al. 1992 Adachi and Hasegawa (proteins coded on mtDNA) 1995 - doublets: Schoeniger and von Haeseler 1994 * computes pairwise maximum likelihood distances for all models $ * automatic recognition of data type * automatic choice of the optimal amino acid model * deals with strictly bifurcating and multifurcating trees * tree search is performed using quartet puzzling, a fast algorithm based on quartet maximum likelihood trees that incorporates an intrinsic replication scheme providing support values for each internal branch. (Strimmer and von Haeseler 1996), (Strimmer, Goldman, and von Haeseler 1996). * as additional input a user tree can be supplied (can be multifurcating) $ * computes ML branch lengths along QP tree or a user tree $ * tree output in CLUSTAL W format, thus allowing to display branch lengths and QP support values for each branch simultaneosly $ * check for homogenity of base composition between the sequences with a chi-square test * estimates TN/HKY model parameters (transition-transversion ratio etc.) $ * lists all unresolved quartets $ From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: DNA programs for Windows Date: 9 Sep 1996 03:41:40 GMT Organization: Best Internet Communications Lines: 38 Message-ID: <5103lk$gao@nntp1.best.com> References: <322FC242.41C6@sgi.celgen.kuleuven.ac.be> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Przemko Tylzanowski (przemko@sgi.celgen.kuleuven.ac.be) wrote: : Yasuhito Abe wrote: : > : > Dear netters, : > I am now launching my molecular work using a newly introduced : > Windows machine. Could somebody introduce me useful : > shareware sites for DNA analysis, such as alignment and : > primer design, using Windows(95)? Thank you for your cooperation. : snip... : isn't it funny that periodically someone asks, BEGS, for decent : share/freeware programs for windows. Programs that would: : - draw simple plasmid maps : - helps in drawing restriction maps from restriction data (gels) : - allows some other, simple data manipulation, such as editing of : sequences, saving them in a few commonly used formats (why the hell : there are so many of them beats me...) etc. : So, it seems that if I would have bought a Mac then I could have all I : want. Is it so difficult to write something for Win95, or simply the : educational strategy of Apple caused that once hooked to it in college : dorm, one just stays with it... It's still taking a little bit of time for Win95 to get the market penetration that MicroSoft would like. The fact is that Win95 is a real improvement on Windows3.1, not least from the point of pre-emptive multitasking, which does make it a candidate system on which to do background bioprocessing; try running Clustalw on a PowerMac and you'll watch the whole machine lockup till the calculation is completed. The other consideration is that Macs *do* play a large role in many universities biocomputing work, and there are a lot of good public and commercial programs available for it. Seems nowadays like many programmers with a biochemistry background are trying to edge in on the commercial market, and I would suggest to you that in a year or so, there are going to be quite a few Win95-specific programs, commercial and free, applied to molecular biology problems like mapping (remember, the next build of Win95 will have a Java run-time built in, which opens up the possibility for useful software tremendously). From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: cor@codon.nih.gov (Cor Witteveen) Subject: HP 8450 Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.99.180 Organization: LNC/NIMH Date: Mon, 9 Sep 1996 16:09:01 GMT Lines: 13 Hi, I'm using a Hewlett Packard 8450A, an old diode array spectrophotometer which is controlled by an internal Hewlett packard computer. The machine is still working fine, but analyzing my data is a drag since I am not able to get the data from the HP computer to a dos or macintosh computer. I was wondering whether anybody has a simple data aquisition program that hooks up a dos computer to the HP 8450A through the RS323 port. Controlling the machine this way is not necessary. Just data aquisition or export of stored data from the HP computer to a dos computer would be fine. please e-mail me directly: cor@codon.nih.gov thanks, Cor From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsxfer2.itd.umich.edu!uunet!in1.uu.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!evolution!thomas From: Thomas Sicheritz Newsgroups: bionet.software Subject: Re: DNA programs for Windows Date: Fri, 6 Sep 1996 23:39:01 +0200 Organization: Uppsala University Lines: 77 Message-ID: References: <322FC242.41C6@sgi.celgen.kuleuven.ac.be> NNTP-Posting-Host: evolution.bmc.uu.se Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: thomas@evolution To: yasuhito@m.ehime-u.ac.jp, przemko@sgi.celgen.kuleuven.ac.be In-Reply-To: <322FC242.41C6@sgi.celgen.kuleuven.ac.be> On Fri, 6 Sep 1996, Przemko Tylzanowski wrote: > Yasuhito Abe wrote: > > > > Dear netters, > > I am now launching my molecular work using a newly introduced > > Windows machine. Could somebody introduce me useful > > shareware sites for DNA analysis, such as alignment and > > primer design, using Windows(95)? Thank you for your cooperation. > snip... > > isn't it funny that periodically someone asks, BEGS, for decent > share/freeware programs for windows. Programs that would: > - draw simple plasmid maps > - helps in drawing restriction maps from restriction data (gels) > - allows some other, simple data manipulation, such as editing of > sequences, saving them in a few commonly used formats (why the hell > there are so many of them beats me...) etc. > > Now, there are a few programs available but: > - anything for plasmid drawing, restriction map making is $$$$$$ > - the is NO PROGRAM (as far as my net searches go)for Win95 that would > take data from single and multiple restriction digests and assemble it > into a restriction map. The only program that I know of that would do > that is included into IG Suite package (Sun or VAX?). And another > program that goes in that direction is DoubleDigester (forgot the > author- sorry) but even that will do only two enzymes. > - there is Sequp but that very efficiently crashes my machine (Pentium > 100, 1Gb hard drive, 32Mb RAM). There was an old version of that program > for DOS, alas, DOS is dead... > > So, it seems that if I would have bought a Mac then I could have all I > want. Is it so difficult to write something for Win95, or simply the > educational strategy of Apple caused that once hooked to it in college > dorm, one just stays with it... > > Przemko > > Just Install Linux (a free Unix clone for the PC), and you can run ALL the big DNA programs (and the small too) I am running on my PC: Linux and Win95. I use following programs: clustalw (alignment) readseq (conversion of sequence files) phylip (phylogenetic analysis) (GDE (Genetic data enviroment)) ACeDB c.elegans (Genome database) xbbtools (visual sequence analysis) seaview (visual alignment editor) phylo_win (visual phylogenetic analysis) blast ( database search) fasta ( -"-) and some 100 more ... If you want to get acces to the major part of free available biology programs ... Install Linux (its a operative system) more info about Linux at http://www.linux.org/ If you have questions mail me thomas@evolution.bmc.uu.se c ya -thomas Sicheritz Ponten Thomas E. UPPSALA UNIVERSITY Vangsbyvaegen 128 S-740 20 Vaenge Biomedical Center Home: +46 18 364358 Department of Molecular Biology BMC: +46 18 174214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://skydancer.bmc.uu.se/~thomas Chaos always defeats order, because it is better organized. (Terry Pratchett) From owner-software@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Emmanuel Skoufos Newsgroups: bionet.software Subject: New gene discovery page Date: 9 Sep 1996 11:31:40 -0700 Organization: Yale University Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear colleagues, This is to announce the availability of a new gene discovery page. The principal site is at: For your convenience there is a European mirror site at: The purpose of this page is to serve as a "desktop" area, primarily for the bench scientist with little biocomputing background. It organizes existing search engines in a coherent, stepwise fashion providing one of the many strategies that may lead to gene discovery. Questions that this page helps to answer are of the type: "Does a particular sequence of DNA code for proteins and what may their function be?" or "Is there a protein in organism A homologous to protein X of organism B?" Please take a moment and visit this site (you will need a forms-capable browser). Your feedback is more than welcome. Sincerely, Emmanuel Skoufos, Ph.D. Yale University School of Medicine Department of Molecular Biophysics and Biochemistry 217 Bass Center P.O.Box 208114 266 Whitney Ave. New Haven, CT 06510-8114 e-mail:skoufs@pantheon.yale.edu phone: (203) 432-6564 or (203) 432-6543 FAX: (203) 432-5175 From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!ptaylor From: ptaylor@hgmp.mrc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: Re: HP 8450 Date: 10 Sep 1996 09:19:36 GMT Organization: MRC Human Genome Resource Centre Lines: 26 Message-ID: <513br8$2cp@mercury.hgmp.mrc.ac.uk> References: NNTP-Posting-Host: tin.hgmp.mrc.ac.uk >I'm using a Hewlett Packard 8450A, an old diode array spectrophotometer >which is controlled by an internal Hewlett packard computer. The machine >is still working fine, but analyzing my data is a drag since I am not able >to get the data from the HP computer to a dos or macintosh computer. I >was wondering whether anybody has a simple data aquisition program that >hooks up a dos computer to the HP 8450A through the RS323 port. >Controlling the machine this way is not necessary. Just data aquisition or >export of stored data from the HP computer to a dos computer would be >fine. Assuming that that should have read RS232, any old terminal software will do. On the Mac, Kermit, Terminal, Microphone & Red Ryder come to mind. I don't know about DOS, but I'm sure there must be dozens. The difficult part is making up a lead for the physical connection. If you want to do this on a mac, mail me for more info. >please e-mail me directly: cor@codon.nih.gov > >thanks, Cor Phil Taylor | MRC Reproductive Biology Unit | Centre for Reproductive Biology | 37 Chalmers Street mbplt@seqnet.dl.ac.uk | Edinburgh EH3 9EW ptaylor@hgmp.mrc.ac.uk | Scotland. From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in1.uu.net!nntp.inet.fi!news.funet.fi!ousrvr3.oulu.fi!paju.oulu.fi!pollanen From: Pollanen Raimo J Newsgroups: bionet.software Subject: Does anyone has any ideas for programs for PC to make database for genetic changes...? Date: Mon, 9 Sep 1996 23:15:45 +0300 Organization: University of Oulu Lines: 21 Message-ID: NNTP-Posting-Host: paju.oulu.fi Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello I am searching for software to make databases (like Access paradox) for very large amount of data of genetic changes (sequences) and same time it should also include data of mutated animals... so ..it should handle a big amount of data...could I use Acces or Paradox for windows or something else...??? Raimo //\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\// // Raimo Pollanen (PhD), Researcher // // Human Papillomavirus Research // // Sinivatukkakuja 10 FIN-90460 Oulunsalo // // Finland // // // // Phone +358-40-5058163, fax +358-81-330687 // // E-mail pollanen@paju.oulu.fi // //\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\// From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!uwm.edu!cs.utexas.edu!nntp.primenet.com!uunet!in2.uu.net!nntp.inet.fi!news.funet.fi!news.utu.fi!newsmaster From: frabli@opal.utu.fi Newsgroups: bionet.software Subject: Does anyone know where I can download F-Prot Pro win95?? Date: Tue, 10 Sep 1996 18:25:18 GMT Organization: University of Turku, Finland Lines: 6 Message-ID: <5138ua$rcd@castor.utu.fi> NNTP-Posting-Host: ib3.tnkpub.utu.fi X-Newsreader: Forte Free Agent 1.0.82 If you know please e-mail me or reply to this posting!!! Thanx, From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.sgi.com!esiee.fr!jussieu.fr!univ-angers.fr!ciril.fr!news.imag.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: plebrun@fysp1.vub.ac.be (Ph. Lebrun) Newsgroups: bionet.software Subject: Re: Lab View Virtual Bench opinions? Date: 10 Sep 1996 13:06:36 GMT Organization: Brussels Free Universities VUB/ULB Lines: 19 Message-ID: <513p4s$85t@rc1.vub.ac.be> References: <32301392.633B@mbox.stetson.edu> NNTP-Posting-Host: fysp1.vub.ac.be X-Newsreader: knews 0.9.3 In article <32301392.633B@mbox.stetson.edu>, barkalow@MBOX.STETSON.EDU (Derek Barkalow) writes: >Would appreciate assistance in finding users of this software in the >undergraduate lab setting. We are setting up a new neurobiology lab and >wonder about the ease of use of Virtual Bench for undergrads? Our >primary goal is to use this SW to replace traditional oscilloscopes. > >Are other software data acquisition and processing systems available >with particular applicability to neurobiology? I found LabView easy to use and was able to get applications for recording EMG and the Hoffman reflex up and running quite quickly. Our 2d year students were quite happy working with a computer and required only a minimum of instructions. If anyone is interested, they can have the VIs. --Philippe From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!SIERRA.NET!mcbrande From: mcbrande@SIERRA.NET ("Marc C. Brande, MS, Founder") Newsgroups: bionet.software Subject: Free Brochure: Cell Bio/Imaging Services at Your Site Date: 10 Sep 1996 10:01:49 -0700 Organization: Cultured Cell Systems (619) 587-4830 FAX: (619) 552-1516 (www.bio.com/co/css.html) (Hands-On As-Needed Cell Biology/Imaging Expertise at Your Site) Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <32353C7E.47FE@sierra.net> Reply-To: mcbrande@sierra.net NNTP-Posting-Host: net.bio.net Email your Full Name/Address/FAX to: mcbrande@sierra.net From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!sol.ctr.columbia.edu!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in2.uu.net!utcsri!utnut!nott!uottawa!bio08!andrew From: "Andrew St. Jean" Newsgroups: bionet.software Subject: adding traces to a Staden project Date: Tue, 10 Sep 1996 09:28:40 -0400 Organization: University d'/of Ottawa Lines: 16 Message-ID: NNTP-Posting-Host: 137.122.25.28 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All, I've been having a problem lately with my copy of the Staden package. When I add trace files to an already existing project, I cannot call up those traces using the trace editor from within the project. I have to start up ted manually and open the SCF file myself. Needless to say, this is very cumbersome. If anyone has any ideas as to what the problem might be, please send me a message at: andrew@bio01.bio.uottawa.ca By the way, I have the 1995.0 version of Staden. Thanks in advance. Andrew St. Jean University of Ottawa From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!biosci!not-for-mail From: bloch@pasteur.fr (Laurent Bloch) Newsgroups: bionet.general,bionet.software Subject: Pasteur Course in Bioinformatics Date: 10 Sep 1996 15:02:43 -0700 Organization: Institut Pasteur, Paris, France Lines: 87 Sender: daemon@net.bio.net Distribution: world Message-ID: <5137rm$htm$3@montespan.pasteur.fr> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23205 bionet.software:16504 Course in informatics offered at the Pasteur Institute. ====================================================== In the series of courses offered at the Pasteur Institute, a course will be offered in informatics in biology. The next session will take place from the 6th of January to the 11th of April 1997. The course description is attached. Registration is mandatory via the committee of courses. Call the secretary of Information and Education of the Pasteur Institute at +33 (1) 45 68 81 40 or via E-mail at algo@pasteur.fr for further information. The working language of the course is French. Tuition costs: a nominal fee, approximately 2 500 French Francs (500 US Dollars). Course Description ================== Informatics in biology ---------------------- The objective of this course is to give to the researchers and future researchers in biology, an initial exposure to informatics. Entry in the course is reserved to those with a degree in biology or an equivalent discipline. With more and more tools available to the biologist, it has become important that the biologist acquire the ability to judge for themselves the usefulness of a new software by the algorithms it employs. The accent is put on the fundamental aspect of this discipline. Two applications in biology will be studied, the analysis of sequences and molecular modeling. The theoretic aspects of informatics will be introduced: programming languages, programing, logic, and also in the technical domain of the system, the network, and computer architecture. Programming is taught according to the functional paradigm (Scheme), but other styles of programming, such as algorithmic and object oriented, will be introduced. The goal of an excellent level of theory will not hurt the acquisition of practical knowledge which will be directly usable in the labratory. The course will consist of lectures and practical sessions. Algorithms and programming lecture 69h Algorithms and programming practical (with Scheme) 52h Theory of Programming languages 9h Object-oriented programming (with SmallTalk) 12h Procedural programming (with Fortran) 6h The programming language C and systems programming 12h Introduction to Unix and X practical 17h History of informatics lecture 6h Perspectives of informatics lecture 10h Algorithms for Biology Algorithms 45h Examples (Sequence analysis & molecular modeling) practical 27h Installation (gcc) 10h Machine architecture and System planning 10h Logic 10h Networks 12h ==================================================================== Total 307h Course Instructors Laurent Bloch William Saurin Frederic Chauveau Harald Wertz Guy Vaysseix Frederique Galisson Irene Wang Daniel Azuelos Eric Gressier Thierry Rose Louis Jones Francoise Balmas Christophe Wolfhugel Stephane Bortzmeyer From owner-software@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!drdave From: lapointe@uthscsa.edu (David S. Lapointe) Newsgroups: bionet.software Subject: Re: Q:Sequence Alignemnt on Win-PC? Date: Tue, 10 Sep 96 17:08:41 GMT Organization: UT Health Science Center San Antonio Lines: 18 Distribution: world Message-ID: <5147gk$69@cosmos.uthscsa.edu> References: NNTP-Posting-Host: drdave.uthscsa.edu X-Newsreader: News Xpress 2.0 Beta #2 In article , Agustin de la Calle wrote: >Hello, > >I was wondering if anybody knows a nice sequence alignmment >program that runs on a PC? > >Thanks for your help! > >Cheers, > Agustin > FASTA (DOS) has several ways of doing alignments. For multiple alignments you could try MACAW (WIN [from ncbi]) or CLUSTALW ( DOS). David Lapointe lapointe@uthscsa.edu > From owner-software@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!cmb.bcm.tmc.edu!solovyev From: solovyev@cmb.bcm.tmc.edu (Victor V. Solovyev) Newsgroups: bionet.software Subject: New high accuracy Protein SS prediction for single sequence Date: 10 Sep 1996 20:46:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 80 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609110345.WAA05239@dove.cellb.bcm.tmc.edu> NNTP-Posting-Host: net.bio.net NEW !!!!!!!!!!! high accuracy SS prediction for single sequences SSPAL- Prediction of protein secondary sturcture by using local alignments Accuracy: Overall 3-states (a, b, c) prediction gives 71% correctly predicted residues on 126 and 471 non-homologous proteins using the jack-knife test procedure. THIS ACCURACY IS REACHED WITHOUT USING MULTIPLE ALIGNMENT INPUT Implemented on WWW: http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html On DEC-alpha it takes a minit,but unfortunately on very loaded Sun Baylor computer you have to wait longer ================================================================================= ================== The other services are =============================================================== FGEBEHB - search for Mammalian gene structure with exons assembling by dynamic programming and using similarity information with known proteins by data base scaning with fasta FEXHB - search for Mammalian coding exons using exon recognition functions and similarity information with known proteins by data base scaning with fasta (the above 2 programs available only by ftp loading to your local computer!!!) You can ftp from gc.bcm.tmc.edu 3 programs for Human and Bacterial gene prediction. The programs better run on DEC_alpha and available from dec_... directories. Variants for Sun OS 5 and OS 4 will be in sun5_.. and sun4_ dirs. Make: ftp gc.bcm.tmc.edu cd pub/solovyev and then cd dec_fgenehb or dec_fexhb or dec_cdsb copy the stuff from these directories to your separate directories. Some additional information about Gene-Finder programs you can get from: WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html FGENEH - search for Mammalian gene structure with exons assembling by dynamic programming FEXH - search for 5'-, internal and 3'-exons HEXON - search for internal exons HSPL - search for splice sites RNASPL - prediction exon-exon junctions in cDNA sequences CDSB - prediction of Bacterial coding regions HBR - recognition of human and bacterial sequences to test a library for E. coli contamination by sequencing example clones TSSG - recognition of human promoter regions (Ghosh/Prestridge motif data) TSSW - recognition of human promoter regions (Weingender motif data base) POLYAH - recognition of of 3'-end cleavage and polyadenilation region of human mRNA precursors FGENED - search for Drosophila gene structure with exons assembling by dynamic programming FEXD - search for Drosophila 5'-, internal and 3'-exons DSPL - search for Drosophila splice sites FGENEN - search for Nematode gene structure with exons assembling by dynamic programming FEXN - search for Nematode 5'-, internal and 3'-exons NSPL - search for Nematode splice sites FGENEA - search for Plant gene structure with exons assembling by dynamic programming FEXA - search for Plant 5'-, internal and 3'-exons ASPL - search for Plant splice sites WWW address: http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html SSP - prediction of a-helix and b-strand in globular proteins by segment-oriented approach. NSSP - prediction of a-helix and b-strand segments in globular proteins by nearest-neighbor algorithm. SSPAL - Prediction of secondary structure by nearest-neighbor method using local alignments PSITE - search for PROSITE patterns with statistics From owner-software@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!csulb.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!uunet!in1.uu.net!nwnews.wa.com!nwfocus.wa.com!redbarn.physio-control.com!haystack.physio-control.com!usenet From: Peter Gadsby Newsgroups: bionet.software Subject: Re: mac printer driver for HP LaserJet 4si? Date: Tue, 10 Sep 96 12:12:19 PDT Organization: Physio Control, Inc. Lines: 3 Message-ID: References: <50mgkv$djr@mserv1.dl.ac.uk> NNTP-Posting-Host: pc_pgadsby.physio-control.com Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage Try the internet at hp.com and download the appropriate drivers. From owner-software@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Mark Miller <70176.1153@CompuServe.COM> Newsgroups: bionet.software,misc.education.home-school.misc,misc.education.science Subject: Free Snake Lecture in Philly! Date: 11 Sep 1996 08:11:33 GMT Organization: Herp-Net 215-464-3562 BBS Lines: 42 Message-ID: <515s7l$91b$3@mhade.production.compuserve.com> Xref: biosci bionet.software:16507 misc.education.home-school.misc:16715 misc.education.science:8432 X- Distribution: PA, NJ, DE PHILADELPHIA HERPETOLOGICAL SOCIETY MEETING NOTICE - ALL ARE WELCOME! Friday, 27 September 1996 - 8:00 p.m. University of Pensylvania, School of Veterinary Medicine 39th & Spruce Streets, Auditorium B-101 "The Biological History of Lampropeltis alterna and the Mexicana Complex Kingsnakes" A two hour slide/lecture by Gerry Salmon Mr. Salmon has been researching kingsnakes (and others) for over 10 years; He is a field associate of the Bronx Zoo; the founder and past VP of the Southern New England Herpetological Society. Mr. Salmon has worked for the Miami Serpentarium and as a natu ralist in South Carolina and New York. He is currently a sergeant in the NY State Police. Please join us for an enjoyable and educational evening! For additional information email MMiller@tjuvm.tju.edu or call the society at 215-464-3561. Regards, Mark Miller, President Philadelphia Herpetological Society The PHS was founded in 1952 by (Professor) Roger Conant; Owns and operates nature preserves in NJ; provides a forum for education and conservation regarding reptiles and amphibians and their habitat; and is recognized as a 501(c)3 non-profit by the IRS. For information on membership, speaking to our group, or our programs, please write to PO Box 52261, Philadelphia PA 19115. From owner-software@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!cronkite.ocis.temple.edu!usenet From: Jim Collins Newsgroups: bionet.software Subject: Grasp and Irix 6.2 Date: Wed, 11 Sep 1996 09:34:57 -0400 Organization: Temple Univ. Lines: 3 Message-ID: <3236C001.41C6@astro.ocis.temple.edu> NNTP-Posting-Host: jcollinsd.bchem.temple.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Does anyone have experience trying Grasp on an Indigo2 with High Impact graphics? I would like to run it on an R10000 under Irix 6.2, but could run it on an R4400 under 5.3 if necessary. Thanks From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!newsfeeder.gi.net!news.mid.net!ink7.ink.org!news.ou.edu!REX.RE.uokhsc.edu!not-for-mail From: ben@REX.RE.uokhsc.edu (Benjamin Z. Goldsteen) Newsgroups: bionet.software Subject: InsightII, Homology -- how do I insert residue? Date: 11 Sep 1996 20:39:34 -0500 Organization: University of Oklahoma Health Sciences Center Lines: 10 Message-ID: <517pkm$g0r@REX.RE.uokhsc.edu> Reply-To: benjamin-goldsteen@uokhsc.edu NNTP-Posting-Host: rex.re.uokhsc.edu X-Newsreader: NN version 6.5.0 CURRENT Hello, I am trying to use Homology to overlay a protein sequence on the backbone of a structure for which I have coordinates. I think I have figured out most of the process except for calculating the coordinates for a residue which is being inserted. I am using Biosym 2.3.5 on an SGI. Thanks! -- Benjamin Z. Goldsteen From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!csn!nntp-xfer-1.csn.net!csn!nntp-xfer-2.csn.net!yuma!purdue!mozo.cc.purdue.edu!macg417f.bio.purdue.edu!user From: cmossman@bilbo.bio.purdue.edu (Cathy Mossman) Newsgroups: bionet.software Subject: pop. genetics programs for microsatellites? Followup-To: bionet.software Date: 11 Sep 1996 20:42:40 GMT Organization: Purdue University Lines: 11 Message-ID: NNTP-Posting-Host: macg417f.bio.purdue.edu Hello, I'm searching for a population genetics program that can calculate allelic frequencies, Fst's (or Slatkin's Rst's) and other general pop. genetics calculations for microsatellite DNA. I'm aware that many people are still using Biosys-1 (Swofford and Selander, 1981), but this earlier version has some limitations when used for microsatellites. Also, it doesn't have a calculation for the corrected Fst (e.g. Slatkin's Rst) that takes into account assumptions critical to microsatellite DNA. If there is an updated Biosys version or other programs that anyone has used for microsatellite data, I would appreciate any help in obtaining a cop. Thanks in advance! Cathy Mossman From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!ringer.cs.utsa.edu!lonestar.jpl.utsa.edu!rtaylor From: rtaylor@lonestar.jpl.utsa.edu (Richard B. Taylor ) Newsgroups: bionet.software Subject: DNA software Date: 12 Sep 1996 14:04:56 GMT Organization: University of Texas at San Antonio Lines: 22 Distribution: world Message-ID: <5195a8$pao@ringer.cs.utsa.edu> NNTP-Posting-Host: lonestar.jpl.utsa.edu Can anyone refer me to software that will let me do various tasks on a DNA sequence such as identify restriction sites, find good primers for sequencing or pcr, identify ORF's and translate the reading frames, and do some multiple alignment? I have seen a program called GeneRunner, and I have heard about one called Oligo. It needs to run on Windows 3.1. I am asking for a friend who is setting up a system. I would like to know if you have used and like the program, what the source and price are, and if support has been good. Thanks for your help, Richard -------------------------------------------------------------------- | Richard B. Taylor, MS | email:rtaylor@lonestar.utsa.edu | | Univ of Texas at San Antonio | phone: (210)-691-5477 | -------------------------------------------------------------------- -- -------------------------------------------------------------------- | Richard B. Taylor, MS | email:rtaylor@lonestar.utsa.edu | | Univ of Texas at San Antonio | phone: (210)-691-5477 | -------------------------------------------------------------------- From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!main.Germany.EU.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software Subject: Re: Does anyone has any ideas for programs for PC to make database for genetic changes...? Date: Thu, 12 Sep 1996 17:57:33 +0200 Organization: EMBL Heidelberg Lines: 26 Distribution: world Message-ID: <323832ED.41C6@EMBL-Heidelberg.DE> References: NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b8Gold (X11; I; IRIX 5.3 IP22) Pollanen Raimo J wrote: > > Hello > > I am searching for software to make databases (like Access paradox) > for very large amount of data of genetic changes (sequences) and > same time it should also include data of mutated animals... > so ..it should handle a big amount of data...could I use Acces or > Paradox for windows or something else...??? > You can user SRS if you have your data in ascii format like embl or swissprot database. SRS address is http://www.embl-heidelberg.de/srs/srsc and you can find more information there. =============================================================== Ramu C | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg Fax: (49) 6221 387517 | Germany http://www.embl-heidelberg.de/~chenna/ ------------------------------------------------------------- From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!solace!news.stealth.net!www.nntp.primenet.com!nntp.primenet.com!news.mathworks.com!fu-berlin.de!irz401!news1.urz.tu-dresden.de!news.uni-leipzig.de!mlucom4.urz.uni-halle.de!newsmaster From: Anne von Fircks Newsgroups: bionet.software,sci.chem,de,sci.chem Subject: sybyl/molcad Date: Thu, 12 Sep 1996 12:14:31 +0000 Organization: Theoretische Chemie MLU Lines: 8 Message-ID: <3237FEA7.3895@mlucom.urz.uni-halle.de> Reply-To: qiecx@mlucom.urz.uni-halle.de NNTP-Posting-Host: mluche1.chemie.uni-halle.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5 (Win16; I) Xref: biosci bionet.software:16514 sci.chem:63855 Who has experience with the MOPAC-Module in SYBYL ? Is it possible to use charges obtained by a ESP calculation in MOPAC 6.0 for the EP properties of the surface? And if yes in which format does sybyl wants this charges ? thanks for help Anne From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.software Subject: RECOMB 97: Call for Posters; Call for Future Sites Proposals Date: 12 Sep 1996 16:34:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 98 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609122314.RAA04338@frodo2.cs.sandia.gov> NNTP-Posting-Host: net.bio.net RECOMB 97 NEWS ************** 1. RECOMB 97: One Extra Day added to the meeting (January 20-23, 1997) 2. Call for Posters: New Feature of RECOMB 97 3. Call for Conference Sites for RECOMB 98 and RECOMB 99 and RECOMB 00 ------------------------------------------------ FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 97) January 20-23, 1997 Eldorado Hotel Santa Fe, New Mexico Sponsored by ACM SIGACT with support from SLOAN Foundation US Department of Energy recomb97@hto.usc.edu http://www.cs.sandia.gov/recomb97 ------------------------------------------- 1. Due to the high quality and quantity of the papers submitted to the conference and a number of invited lectures as well as a variety of other events scheduled for the conference we have decided to add a fourth day to the conference. The new dates are January 20-23, 1997. 2. By popular demand we are adding a new feature to the conference. Call for RECOMB 97 Posters ************************** Please send a one-page abstract of your Poster including title, author(s), affiliation and abstract-text *preferably* via email to recomb97@hto.usc.edu or hard copy to: Professor Michael Waterman RECOMB 97 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 Deadline for poster abstract submission: October 25, 1996 Notification of acceptance/rejection: November 15, 1996 3. The RECOMB Conference needs Sites for 1998, 1999, and 2000. As reserving hotels in some locations requires arrangements made one or two years in advance, we are soliciting proposals now for the next sites. Please send us email with proposals for locations for the next RECOMB both in US as well as outside US. At the RECOMB 97 business meeting we will discuss these matters in detail. We hope to see you all at RECOMB 97 in Santa Fe. Mike Waterman Pavel Pevzner Sorin Istrail The RECOMB Executive Committee From owner-software@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!clicnet!news.clic.net!usenet From: yobodich@total.net (Yobodich) Newsgroups: bionet.software Subject: help me please Date: Thu, 12 Sep 1996 22:34:47 GMT Organization: Famille Maheu Lines: 12 Message-ID: <519oom$8vq@clic3.qbc.clic.net> Reply-To: yobodich@total.net NNTP-Posting-Host: poste05.prospection.qc.ca X-Newsreader: Forte Free Agent 1.0.82 Help! I have to convert some MAC writenow files into some ascii files for PC. Is someone can help me? Please, it's a rush! Thanks! Yobodich tmaheu@prospection.qc.ca From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!BENPC.BIONET.NSC.RU!ptitsyn From: ptitsyn@BENPC.BIONET.NSC.RU ("Andrey A.Ptitsyn") Newsgroups: bionet.software Subject: Re: DNA software Date: 12 Sep 1996 21:43:48 -0700 Organization: Institute of Cytology and Genetics, Novosib Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609130442.LAA20625@benpc.bionet.nsc.ru> NNTP-Posting-Host: net.bio.net Have a look at our anonymous FTP: ftp://ftp.bionet.nsc.ru There you can find a number of Windos programs and packages for most things you ask for, i.e. multiple alignment, ORF translation, etc. Andrey A. Ptitsyn From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!news.uwa.edu.au!usenet From: Jane Sampson Newsgroups: bionet.software Subject: FREQPARS Date: 13 Sep 1996 07:58:45 GMT Organization: The University of Western Australia Lines: 4 Message-ID: <51b47l$5ra@enyo.uwa.edu.au> NNTP-Posting-Host: mac55.botany.uwa.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:bionet.software Does anyone have a copy of Swofford and Berlocher's (1987) FREQPARS compiled for more than 10 alleles? Thanks. Jane From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!news.eecs.uic.edu!uicvm.uic.edu!news.cc.uic.edu!usenet From: levenson@uic.edu (Victor Levenson) Newsgroups: bionet.software Subject: Re: DNA software Date: Fri, 13 Sep 1996 17:39:06 GMT Organization: University of Illinois at Chicago Lines: 36 Message-ID: <51c5vn$1beo@piglet.cc.uic.edu> References: <5195a8$pao@ringer.cs.utsa.edu> NNTP-Posting-Host: e128.gene.uic.edu X-Newsreader: Forte Free Agent 1.0.82 rtaylor@lonestar.jpl.utsa.edu (Richard B. Taylor ) wrote: >Can anyone refer me to software that will let me do various tasks >on a DNA sequence such as identify restriction sites, find good >primers for sequencing or pcr, identify ORF's and translate the >reading frames, and do some multiple alignment? I have seen a >program called GeneRunner, and I have heard about one called Oligo. >It needs to run on Windows 3.1. I am asking for a friend who is setting >up a system. I would like to know if you have used and like the >program, what the source and price are, and if support has been good. >Thanks for your help, >Richard Richard: I have used for some time now program called CLONE: it can identify RE sites, ORFs, cut, ligate etc. It has a companion ENHANCE, which gives you a decent number of ways to present your cloning stratagy, etc, and yet another companion, PRIMER, which helps in primer design and is rather flexible. All this package is distributed (maybe even written) by Scientific and Educational Software. Last time I saw their catalogue it was about $400 (clone) $300(enhance) and $200(primer). If you are interested I will send you their phone#. Usual disclaimers ;-): I have nothing to do with them but use their product. Cheers, Victor From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!EU.net!newsfeed.internetmci.com!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Molecular Modeling programs on different platforms - table correct? Date: 13 Sep 1996 22:33:06 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 41 Message-ID: <51cnf2$mr0@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Hi, Periodically I check the status of various molecular modeling/molecular display/related programs with respect to portability. This is my latest table - if anybody sees any errors or wants to add something, please chime in. Listed alphabetically MIPS ---DEC Alpha---- Intel What SGI DU WNT Windows GraphicsType Biosym Yes No* No* No* GL Grasp Yes No No No GL MidasPlus Yes No No No GL molmol Yes Yes No No X11 O Yes No No No GL rasmol Yes Yes ? Yes X11/Windows Setor Yes No No No GL VMD Yes No No No GL XtalView Yes Yes No No GL/X11 * Separately licensed "Axxess" product lets Biosym run as an X11 client. Kind of amazing to me that more of these have not been ported to other platforms, for instance Alpha/Linux or WNT. Looks like the only really portable one is Rasmol. In terms of horsepower the SGIs are at least twice as expensive as these alternatives. I guess the ports will only come when the grants start coming back marked with "buy cheaper platforms". If I get a vote, I cast it for moving to WNT. Not that I'm a big fan of that OS, but realistically, WNT workstations would be a lot more readily accepted by our undergrads then the current set of SGIs are, and getting other software for WNT machines (word processors and so forth) would be one heck of a lot easier and lots cheaper than it is for SGIs. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!cronkite.ocis.temple.edu!usenet From: "Jimmy H. Collins" Newsgroups: bionet.software Subject: Grasp and Irix 6.2 Date: Fri, 13 Sep 1996 13:58:09 -0600 Organization: Temple University Lines: 4 Message-ID: <3239BCD1.35@astro.ocis.temple.edu> Reply-To: jcollins@astro.ocis.temple.edu NNTP-Posting-Host: jcollinsc.bchem.temple.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Does anyone have experience trying Grasp on an Indigo2 with High Impact graphics, especially on an R10000? I would like to run it on an R10000 under Irix 6.2, but could run it on an R4400 under 5.3 if necessary. Thanks From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!rain.fr!news.remcomp.fr!invivo!eWattel.lille From: eWattel.lille@invivo.remcomp.fr (Eric Wattel) Reply-To: eWattel.lille@invivo.remcomp.fr Newsgroups: bionet.software Distribution: world Subject: search program macintosh Date: 13 Sep 1996 09:33:50 GMT Message-ID: <1170083735.256679@invivo.remcomp.fr> Organization: inVivo Lines: 12 Hello, I was wondering if anybody knows a nice sequence alignmment and PCR (to select primers and probes) program that runs on a MACINTOSH? Thanks for your help! EW eWattel.lille@invivo.edu end ******************************************************************** Sent by inVivo. The BBS of Life Sciences, Paris, France, info@invivo.edu From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!nntp.primenet.com!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!newsfeed.internetmci.com!netnews.nwnet.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.software Subject: CrossMatcher: A Sequence Comparison Program for the Mac Date: 13 Sep 1996 08:43:18 GMT Organization: University of Washington, Seattle Lines: 54 Message-ID: <51b6r6$cgi@nntp3.u.washington.edu> NNTP-Posting-Host: saul4.u.washington.edu NNTP-Posting-User: roach As if we needed another one, right? However, I have found it useful, as have others in my lab, so I felt it would only be fair to share it with everyone. So here's the help text from CrossMatcher, which should speak for itself: This is a little Hypercard stack written to assist in comparing a set of DNA sequences with each other. It is primarily designed to do cDNA comparisons, as there is an (arbitrary) limit of 1498 bp on sequence lengths (sequences can be longer but are ignored beyond 1498 bp). No returns or spaces or other characters should be in the sequence files (or they will be treated as data). Crossmatcher uses the dynamic clipping XFCN "DynaClip" which I wrote and is more fully described in my "DynaClip" stack. Double-clicking on a highlighted selection in the results window brings up a dynamic alignment of each sequence along with the score of that alignment (which should be the same as the local alignment score - if not, you either need to increase the maximum alignment length or do a dot plot with some other program to unscramble multiple similarities) The entry for maximum alignment cannot be set above 1999. This is the maximum length that my XFCN DynaAlign can handle. However, this requires 8 Mb of RAM in addition to what HyperCard normally uses, so if you have HyperCard set to less RAM, you will want to cut back to around the default of 400, which requires less than 400 Kb of RAM in addition to the 1-2 Mb HyperCard needs. The amount of RAM needed is proportional to the square of the sequence length. I strongly recommend using the default values for gap penalty, mismatch score, and match score. Adjusting the threshold will alter the number of matches returned. Setting it to "1" will return all matches. You can find CrossMatcher at: http://weber.u.washington.edu/~roach/Programs/ Hopefully, someone will find it useful. ------------------------------------------------------------------ Jared C. Roach Department of Molecular Biotechnology Health Sciences Building, Room K354 University of Washington Box 357730 Seattle, WA 98195 phone (206) 616-4536 FAX (206) 685-7301 roach@u.washington.edu http://weber.u.washington.edu/~roach/ From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-peer.sprintlink.net!newsfeed.internetmci.com!in2.uu.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.software Subject: DynaClip: An End-Clipping Program for the Mac Date: 13 Sep 1996 08:36:36 GMT Organization: University of Washington, Seattle Lines: 58 Message-ID: <51b6ek$cd6@nntp3.u.washington.edu> NNTP-Posting-Host: saul4.u.washington.edu NNTP-Posting-User: roach As if we needed another one, right? However, I have found it very useful, as have others in my lab, so I felt it would only be fair to share it with everyone. So here's the help text from DynaClip, which should speak for itself: DynaClip is a program designed to trim a little bit off of the 5' and 3' ends of DNA sequence reads. These will be simple text files - no returns - no spaces - no GCG format or anything. The ".Seq" files produced by an ABI automated DNA sequencer are a fine example of what I'm talking about here. Now DynaClip is a fine program and will do a nice job. But, if you are an idealist, you will only mask regions of your sequence that don't interest you, and save everything else. End-clipping is retro, and should be considered a throwback to the past. However, sometimes the future is a little slow to arrive and be universally implemented. We find DynaClip tremendously useful to munch our cDNA sequences before we search them against a database. We find that SearchLauncher is an excellent downstream application from DynaClip. And then HTTP_Directory_Maker is useful to catalog the SearchLauncher output. Enjoy. Probably the nicest thing about DynaClip is that it does an almost perfect job of getting rid of the portion (hopefully its just a portion) of your sequence that is vector sequence. If you have a really short insert, it will get rid of your vector both 5' and 3'. SInce it uses dynamic alignment, this end clipping works even if the cloning site is missing (i.e. chewed back or the like) or was compressed (a common cloning site occurence). DynaClip also produces a nice output so you can see your clipping statistics. DynaClip ships with the Strategene lambda-ZAP cloning site sequences - if you're using another vector, you'll have to input the sequences appropriate to your vector. DynaClip does not mask regions of low complexity. I don't even know the right algorithm to use to do that. You can find DynaClip at: http://weber.u.washington.edu/~roach/Programs/ Hopefully, someone will find it useful. ------------------------------------------------------------------ Jared C. Roach Department of Molecular Biotechnology Health Sciences Building, Room K354 University of Washington Box 357730 Seattle, WA 98195 phone (206) 616-4536 FAX (206) 685-7301 roach@u.washington.edu http://weber.u.washington.edu/~roach/ From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!nntp.primenet.com!enews.sgi.com!newshub1.home.net!ames!lll-winken.llnl.gov!fnnews.fnal.gov!unixhub!news.Stanford.EDU!not-for-mail From: peterc@camelot.Stanford.EDU (Peter Covitz) Newsgroups: bionet.software Subject: Re: search program macintosh Date: 13 Sep 1996 10:59:50 -0700 Organization: Stanford University, CA 94305, USA Lines: 8 Message-ID: <51c7em$50d@camelot.Stanford.EDU> References: <1170083735.256679@invivo.remcomp.fr> NNTP-Posting-Host: camelot.stanford.edu Lasergene, a modular program package by the company DNASTAR is not bad. It has a decent sequence alignment module that uses the Clustal method. It also has a PCR primer selection module, but I haven't tried it out. You can get more info from them at sales@dnastar.com Peter Covitz From owner-software@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!nntp.primenet.com!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!news From: kbeler@gpu.srv.ualberta.ca (KB) Newsgroups: bionet.software Subject: Help - looking for a slideshow presentation program Date: Fri, 13 Sep 1996 15:23:12 GMT Organization: University of Alberta, Edmonton, Canada Lines: 31 Message-ID: <51c573$8uq@pulp.ucs.ualberta.ca> NNTP-Posting-Host: async1-9.remote.ualberta.ca X-Newsreader: Forte Free Agent 1.0.82 I am looking for a DOS based program that will initiate a slide show of graphic files that have been pre-selected for it. If it can play .wav files through a PC speaker that would be great. Basically I am preparing a presentation for a university class project. I need to be able to have the autoexec file start a program as soon as the computer is turned on and for that program to initiate a slide show of graphic files (.gif or .jpg) th