From owner-repertoires@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!bcc.ac.uk!peer-news.britain.eu.net!xara.net!news.cais.net!primus.ac.net!imci4!newsfeed.internetmci.com!howland.reston.ans.net!news5.ner.bbnplanet.net!news.ner.bbnplanet.net!das-news2.harvard.edu!fas-news.harvard.edu!fas.harvard.edu!rickles From: rickles@fas.harvard.edu (Richard Rickles) Newsgroups: bionet.molecules.peptides,bionet.molecules.repertoires Subject: FENTOMOLE PROTEIN SEQUENCING Date: 4 Feb 1996 15:15:09 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 8 Message-ID: <4f2iht$lsm@decaxp.harvard.edu> NNTP-Posting-Host: fas.harvard.edu X-Newsreader: NN version 6.5.0 #3 (NOV) Xref: biosci bionet.molecules.peptides:179 bionet.molecules.repertoires:92 FEMTOMOLE PROTEIN SEQUENCING-Means you CAN identify those proteins on PVDF from 2D gels and minigels... contact brauer@ariad.com (include your fax number) From owner-repertoires@net.bio.net Fri Feb 09 22:00:00 1996 Path: biosci!biosci!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.molecules.peptides,bionet.molecules.repertoires Subject: Re: FENTOMOLE PROTEIN SEQUENCING Date: 10 Feb 1996 07:28:13 -0800 Organization: BIOSCI International Newsgroups for Biology Lines: 11 Distribution: world Message-ID: <4fidid$ldh@net.bio.net> References: <4f2iht$lsm@decaxp.harvard.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molecules.peptides:185 bionet.molecules.repertoires:93 We do not allow advertising on the bionet newsgroups and I wonder if Harvard permits the use of its facilities for this purpose. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-repertoires@net.bio.net Sun Feb 11 22:00:00 1996 Path: biosci!daresbury!daresbury!not-for-mail From: Troels Wind Newsgroups: bionet.molecules.repertoires Subject: Ton Logtenberg? Date: 12 Feb 1996 11:42:09 -0000 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Message-ID: <4fn92h$gnp@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk (molreps) Hi all, Does any of you know the e-mail adress of Ton Logtenberg, University of Utrecht (The Netherlands)? He made the scFv phage display library described in JMB (1995) 248, p 97-105. Thanks in advance! Troels Wind University of Aarhus Denmark From owner-repertoires@net.bio.net Sun Feb 11 22:00:00 1996 Path: biosci!daresbury!daresbury!not-for-mail From: "Janet Clench, Library, Tel:(39 6)91093220" Newsgroups: bionet.molecules.repertoires Subject: Another search on molecular repertoires for your delight ... Date: 12 Feb 1996 10:12:26 -0000 Lines: 145 Sender: lpddist@mserv1.dl.ac.uk Message-ID: <4fn3qa$bu6@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk ****************************************************** Subject: Combinatorial & Phage Libraries Date: January 22, 29, February 5 1996 ****************************************************** Biochemical Society Transactions 23: 4 (NOV 1995) ME Verhoeyen, CPE Vanderlogt, TS Beggs, PJ Davis Antibody fragments for controlled delivery of therapeutic agents 1067-1073 Molecular Immunology 32: 14-15 (OCT 1995) S Portolano, MF Prummel, B Rapoport, SM Mclachlan Molecular cloning and characterization of human thyroid peroxidase autoantibodies of lambda light chain type 1157-1169 Gene 166: 2 (DEC 12 1995) ND Grihalde, YCJ Chen, A Golden, E Gubbins, W Mandecki Epitope mapping of anti-HIV and anti-HCV monoclonal antibodies and characterization of epitope mimics using a filamentous phage peptide library 187-195 Molecular & General Genetics 249: 4 (DEC 10 1995) G Petersen, DY Song, B Hugledorr, I Oldenburg, EKF Bautz Mapping of linear epitopes recognized by monoclonal antibodies with gene-fragment phage display libraries 425-431 Journal of Neuroscience Methods 62: 1-2 (NOV 1995) DC Merz, RJ Dunn, P Drapeau Generating a phage display antibody library against an identified neuron 213-219 FEBS Letters 377: 2 (DEC 18 1995) C Krebber, S Spada, D Desplancq, A Pluckthun Go-selection of cognate antibody-antigen pairs by selectively-infective phages 227-231 Protein Engineering 8: 10 (OCT 1995) LK Johansen, B Albrechtsen, HW Andersen, J Engberg pFab60: A new, efficient vector for expression of antibody Fab fragments displayed on phage 1063-1067 Clinical and Experimental Immunology 102: 3 (DEC 1995) R Finnern, JM Bye, KM Dolman, MH Zhao, A Short, JD Marks, MC Lockwood, WH Ouwehand Molecular characteristics of anti-self antibody fragments against neutrophil cytoplasmic antigens from human V gene phage display libraries 566-574 International Immunology 7: 12 (DEC 1995) H Schild, U Gruneberg, G Pougialis, HJ Wallny, W Keilholz, S Stevanovic, HG Rammensee Natural ligand motifs of H-2E molecules are allele specific and illustrate homology to HLA-DR molecules 1957-1965 Biochemical Pharmacology 50: 12 (DEC 22 1995) JX Meng, TR John, II Kaiser Specificity and binding affinity of an anti-crotoxin combinatorial antibody selected from a phage- displayed library 1969-1977 Biochemical Journal 313: Part 1 (JAN 1 1996) SE Blondelle, E Takahashi, RA Houghten, E Perezpaya Rapid identification of compounds with enhanced antimicrobial activity by using conformationally defined combinatorial libraries 141-147 Journal of Biological Chemistry 270: 52 (DEC 29 1995) BL Webb, MM Cox, RB Inman An interaction between the Escherichia coli RecF and RecR proteins dependent on ATP and double- stranded DNA 31397-31404 Journal of Biological Chemistry 271: 1 (JAN 5 1996) EL Martin, S Rensdomiano, PJ Schatz, HE Hamm Potent peptide analogues of a G protein receptor- binding region obtained with a combinatorial library 361-366 Angewandte Chemie - International Edition in English 34: 23-24 (JAN 5 1996) J Sadowski, M Wagener, J Gasteiger Assessing similarity and diversity of combinatorial libraries by spatial autocorrelation functions and neural networks 2674-2677 Angewandte Chemie - International Edition in English 34: 23-24 (JAN 5 1996) HP Wessel, CM Mitchell, CM Lobato, G Schmid Saccharide-peptide hybrids as novel oligosaccharide mimetics 2712-2713 Angewandte Chemie - International Edition in English 34: 23-24 (JAN 5 1996) O Kanie, F Barresi, YL Ding, J Labbe, A Otter, LS Forsberg, B Ernst, O Hindsgaul A strategy of ''random glycosylation'' for the production of oligosaccharide libraries 2720-2722 Tetrahedron Letters 37: 1 (JAN 1 1996) S Sasaki, M Takagi, Y Tanaka, M Maeda A new application of a peptide library to identify selective interaction between small peptides in an attempt to develop recognition molecules toward protein surfaces 85-88 Tetrahedron Letters 37: 1 (JAN 1 1996) M Cardno, M Bradley A simple multiple release system for combinatorial library and peptide analysis 135-138 Research in Immunology 146: 6 (JUL-AUG 1995) P Lafaye, F Nato, JC Mazie, N Doyen Similar binding properties for a neutralizing anti- tetanus toxoid human monoclonal antibody and its bacterially expressed Fab 373-382 From owner-repertoires@net.bio.net Sun Feb 11 22:00:00 1996 Path: biosci!daresbury!daresbury!not-for-mail From: Andrew Wallace Newsgroups: bionet.molecules.repertoires Subject: Call for papers - forwarded from molmodel Date: 12 Feb 1996 08:26:23 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Message-ID: <4fmtjf$6u9@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk Forwarded message from molmodel Andrew In bionet.molec-model Msg # 803 Mark Murcko wrote: ===== CALL FOR PAPERS ===== Session on De Novo Ligand Design American Chemical Society Annual Meeting Orlando, Florida, August, 1996 I am looking for papers (both oral presentations and posters) on the subject of the design and use of ligand design software. Previously unpublished methods, as well as novel applications of de novo methods, are especially welcome. If you would like to present a talk or a poster at this session, please send email to the address shown below. Dr. Mark Murcko Senior Scientist Vertex Pharmaceuticals markm@vpharm.com From owner-repertoires@net.bio.net Mon Feb 12 22:00:00 1996 Path: biosci!DARTMOUTH.EDU!Pamela.J.Buchli From: Pamela.J.Buchli@DARTMOUTH.EDU (Pamela J. Buchli) Newsgroups: bionet.molecules.repertoires Subject: phage display- deletions Date: 13 Feb 1996 09:47:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <25029663@dancer.Dartmouth.EDU> NNTP-Posting-Host: net.bio.net I am displaying protein analogs using phage display but have been finding many unwanted deletions in the DNA sequence of the proteins after a single round of affinity selection. Is anyone else seeing this? I am suspecting that the deletions are occuring during amplification of the phage. What is the general length of time used to amplify phage? In the literature I've read 18-24 hours but would like to know what others have found to work. I am using a phagemid vector that contains a cassette which was randomized at 12 nucleotides and amplified using PCR (I used PFU polymerase) so it is possible that some mutations are being made during the PCR reaction. I have sequenced clones in the original library and do not see the same number of deletions as I do in the subsequent clones isolated after the affinty selection process. I would appreciate any ideas or advice! Cheers, Pam Buchli iguana@dartmouth.edu From owner-repertoires@net.bio.net Wed Feb 14 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!tube.news.pipex.net!pipex!dish.news.pipex.net!pipex!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!kjaer From: kjaer@biobase.dk (Svend Kjaer) Newsgroups: bionet.molecules.repertoires Subject: Epitope mapping of ScFv's? Date: 15 Feb 1996 20:20:29 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 19 Message-ID: <4g04id$idq@news.uni-c.dk> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Hi I am for no particular reason curious to know if anybody out there in the phage community has ever tried or heard of people epitopemapping their phage-displayed and selected scFv or Fabs by means of phage display, i.e. by the use of peptidelibraries. I haven't seen any reports of this kind and wonder why ?. Of course, I'm thinking of the soluble forms of scFv or Fabs, not the displayed ones. Any input appreciated Svend Kjaer, Ph.D-student Institute of Molecular and Structural Biology Dept. of Chemistry University of Aarhus Denmark From owner-repertoires@net.bio.net Sun Feb 18 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: ilag@morph.spacenet.de (Vic Ilag) Newsgroups: bionet.molecules.repertoires Subject: yeast 2-hybrid patent Date: 19 Feb 1996 14:14:03 -0000 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ga0jb$n3n@mserv1.dl.ac.uk> X-Sender: mo1010@mail.spacenet.de (Unverified) Original-To: molreps@dl.ac.uk Hi, Can anyone refer me to the original patent (if any) for the yeast 2-hybrid system or any patent that covers it ? Please email me ilag@morphosys.spacenet.de THanks in advance. vic From owner-repertoires@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: jose luis toran Newsgroups: bionet.molecules.repertoires Subject: fab purification Date: 20 Feb 1996 21:32:42 -0000 Organization: cnb Lines: 2 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4gdelq$4df@mserv1.dl.ac.uk> X-URL: http://www.bio.net:80/hypermail/MOLECULAR-REPERTOIRES/9601/0000.html MIME-Version: 1.0 Original-To: molreps@dl.ac.uk I have any problem to purified soluble fab with a anti human fab column ¿you now any comercial anti human fab colunm that work? From owner-repertoires@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!news.Stanford.EDU!tera.mcom.com!news.uoregon.edu!news.dacom.co.kr!news.kreonet.re.kr!news.nuri.net!imci2!imci3!imci4!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!news From: msz@bmc.uu.se (Michael Szardenings) Newsgroups: bionet.molecules.repertoires Subject: Re: phage display- deletions Date: 20 Feb 1996 13:03:21 GMT Organization: University Uppsala, Sweden Lines: 50 Distribution: world Message-ID: <4gcgqp$29ku@columba.udac.uu.se> References: <25029663@dancer.Dartmouth.EDU> NNTP-Posting-Host: msz.bmc.uu.se Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 In article <25029663@dancer.Dartmouth.EDU>, Pamela.J.Buchli@DARTMOUTH.EDU says... > > >I am displaying protein analogs using phage display but have been finding many >unwanted deletions in the DNA sequence of the proteins after a single round of >affinity selection. Is anyone else seeing this? I am suspecting that the >deletions are occuring during amplification of the phage. What is the general >length of time used to amplify phage? In the literature I've read 18-24 hours >but would like to know what others have found to work. I am using a phagemid >vector that contains a cassette which was randomized at 12 nucleotides and >amplified using PCR (I used PFU polymerase) so it is possible that some >mutations are being made during the PCR reaction. I have sequenced clones in >the original library and do not see the same number of deletions as I do in the >subsequent clones isolated after the affinty selection process. I have been doing something very similiar and tried the method first with a non randomized sequence, to establish panning procedures with something that should work. I observed the same problem even with the non-randomized oligos. The reasons I could figure out so far are probably instabilities of E.c. when certain sequences are expressed. I got much less truncations in some strains than in others. Probably the oligo used was not too pure from the beginning and contained some incomplete sequences. Clones containing these probably grew better than all others. Its getting much worse right now with a randomised sequence, but I am still checking out the oligo in that case. I have been using VentPol from Biolabs, but the cause of these problems may not be the PCR itself (?). About amplification: 1 O.D. E.c. produces about 1E10-1E11 phages or phagemids per hour, or in other words each rescued phage will probably produce up to 100 new phages per hour. Always depending on how happily the bugs grow at all. Its probably your choice how long you grow them. Regards Michael ========================================================================= * * ****** ******** ********************************************* ** ** *** ** ******** * Michael Szardenings * *** *** ***** *** * Biomedical Center, Pharm. Pharm. * **** **** ***** *** * Box 591 Tel.:int46-18-17422* ** *** ** ** *** ******** * S-751 24 Uppsala FAX :int46-18-55971* ** * ** ****** ******** ********************************************* ========================================================================= INTERNET : MSZ@bmc.uu.se ========================================================================= From owner-repertoires@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!CLDX.COM!Mark.Sullivan From: Mark.Sullivan@CLDX.COM ("Mark Sullivan") Newsgroups: bionet.molecules.repertoires Subject: Position available Date: 20 Feb 1996 05:45:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Subject: Time: 8:30 AM OFFICE MEMO Position available Date: 2/20/96 Johnsson & Johnson Clinical Diagnostics has an opening for a Ph.D. Molecular Biologist with experience in antibody engineering and phage display. Send inquiries by email to MSulliva@cldx.com. From owner-repertoires@net.bio.net Tue Feb 27 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molecules.repertoires Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 28 Feb 1996 02:00:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602281000.CAA25647@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ---------------------------------------------------------------------- From owner-repertoires@net.bio.net Wed Feb 28 22:00:00 1996 Path: biosci!mmd.com!jimostrem From: jimostrem@mmd.com (Jim Ostrem) Newsgroups: bionet.molecules.repertoires Subject: alignment program? Date: 29 Feb 1996 07:57:48 -0800 Organization: Hoechst Marion Roussel Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602291554.AA02870@gate.mmd.com> NNTP-Posting-Host: net.bio.net I am looking for a simple protein sequence alignment program that will calculate similarity as well as identity. Preferably it would be one that would allow me to set D=E, K=R, L=I=V, etc as I wish. Anyone know of a DOS or Windows based program, and where to find it?? Thanks, Jim From owner-repertoires@net.bio.net Thu Feb 29 22:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!sgigate.sgi.com!imci3!imci4!newsfeed.internetmci.com!cdc2.cdc.net!uunet!in2.uu.net!scanner.worldgate.com!ve6bc!alberta!rover.ucs.ualberta.ca!gallin.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molecules.repertoires Subject: Re: alignment program? Date: Fri, 1 Mar 96 01:41:50 GMT Organization: University of Alberta Lines: 23 Distribution: world Message-ID: References: <199602291554.AA02870@gate.mmd.com> NNTP-Posting-Host: gallin.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 My understanding of most of the alignment programs is that they use a scoring matrix to generate aan alignment score, and then minimize it. All you need to do in that case is generate a new scoring matrix that provides a zero or near zero score for the matches that you mention. Actually, there are probably scoring matrices that already do this. Maybe you should look at the alignment package that you currently use and see how you can go about changing the scoring matrix. In Article <199602291554.AA02870@gate.mmd.com>, jimostrem@mmd.com (Jim Ostrem) wrote: >I am looking for a simple protein sequence alignment program that will >calculate similarity as well as identity. Preferably it would be one that >would allow me to set D=E, K=R, L=I=V, etc as I wish. Anyone know of a >DOS or Windows based program, and where to find it?? > >Thanks, > Jim > > Warren Gallin, Department of Biological Sciences, University of Alberta wgallin@gpu.srv.ualberta.ca