From owner-embldatabank@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-hub.sprintlink.net!news.sprintlink.net!news-stk-11.sprintlink.net!news.dx.net!portal.dx.net!not-for-mail From: Xtra_Cash@your.home.com (MoMoney) Newsgroups: bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genbank Subject: Earn extra cash for the holidays working from home. Date: 2 Dec 1996 20:42:35 -0500 Organization: Work from Home Network Lines: 13 Sender: user@portal.dx.net Message-ID: <5800ib$ek@portal.dx.net> Reply-To: No one! NNTP-Posting-Host: portal.dx.net Xref: biosci bionet.molbio.bio-matrix:803 bionet.molbio.embldatabank:725 bionet.molbio.evolution:5391 bionet.molbio.gdb:539 bionet.molbio.genbank:2433 Homeworkers Urgently Needed! Earn weekly paychecks from the comfort of your home. 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Send long, self-addressed, stamped envelope to: S.P.E.L., Dept IN-2 PO Box 211-111 Royal Palm Bch, FL 33421-1111 From owner-embldatabank@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!158.250.39.26!Gamma.RU!srcc!news.phys.msu.su!mx.nsu.ru!usenet From: Stanislav <374rsj@cceco.nsu.ru> Newsgroups: bionet.molbio.embldatabank Subject: Angiogenin Date: Thu, 05 Dec 1996 19:21:08 -0800 Organization: nsu Lines: 82 Message-ID: <32A79124.35F8@cceco.nsu.ru> Reply-To: 374rsj@cceco.nsu.ru NNTP-Posting-Host: ws38.cceco.nsu.ru Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win16; I) Scientists, businessmen and simply interested in research and promotion of new bioengineering materials, we can offer you angiogenin that is the result of our last successful research project. 1. The independent private enterprise "Biok" was founded by scientists and businessmen for the purpose of realization and commercial application of the intellectual property of the founders. We would like to offer you the angiogenin substance and biotechnological method for its production. 2.Angiogenin is a member of angiogenic proteins-substances, which stimulates the growth of the blood vessels. Angiogenin is a basic single-chain protein of about 14 kD. It consists of 123 amino acids. In contrast to other angiogenic substances angiogenin has no direct mitogenic effect on fibroblast and endothelial cells, although it binds to endothelial cells of blood vessels. Angiogenin possesses strong angiogenic activity in biological assays ( in choricallantoic membrane of developed chicken and on rabbit corneal ) at dose as low as 1-5 ng. Mechanisms of its actions and physiological roles are being investigated. Nevertheless it's clear now that thanks to its' remarkable effects angiogenin seems to be a good substance for development of efficient drug on its base. It can be used for healing of wounds, for treatment of the cerebral thrombosis and myocardial infarction and other pathological conditions which are caused by neovasoularization disturbances. More over, on the base of the substance new diagnostic kits for detection of angiogenin presence in human tissue and biological fluids may be constructed as well as radioreceptor assay. 3. We have developed the original technology for production of angiogenin. Human recombinant angiogenin obtained is synthesized by original recombinant bacterial strain. It is of high biochemical and immunochemical purity and possesses high biological activity. Substance could be used for research goals. At present the preclinical trials of produced angiogenin is being carried out. 4. Our firm has developed and produced a bioreactor of a new type for suspension cultivation of tissue cells and recombinant bacterial strain. The bioreactor embodies a new principle of stirring a cell suspension without a stirrer. The suspension is agitated by creating quasi-stationary three-dimensional motion similar to a otating vortex ring, generated by the aerating gas flow. 5. The novelty of recombinant bacterial strain and bioreactor are protected by patents in Russia. 6. We would like to offer you : - supply angiogenin as biomaterial for your laboratories and other needs. - sale of bioreactor with working volume 5 and 10 dm^3 - "Biok" is interested in partners for organization joint ventures producing angiogenin substance. - "Biok" is interested in partners for organization joint ventures producing bioreactors mentioned above. We are ready to listen to your any idea upon that subject. Sincerely yours, Yuri Ramazanov, Director of "Biok" Prof. Nikolai P. Mertvetsov, M. D. Ph. D, Deputy Director of Novosibirsk Institute of Bioorganic Chemistry, head of department of clinical research From owner-embldatabank@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 6 Dec 1996 02:03:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612061000.CAA05471@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. 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. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-embldatabank@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "E. Kolker" Newsgroups: bionet.general,bionet.info-theory,bionet.molbio.proteins,sci.med.pharmacy,bionet.molbio.embldatabank,bionet.population-bio,bionet.molbio.evolution,sci.bio.systematics,bionet.software Subject: New deadline & Web site Date: 6 Dec 1996 05:44:32 -0800 Organization: University of Washington Lines: 88 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <327E21BF.167E@bioinformatics.weizmann.ac.il> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:24391 bionet.info-theory:4414 bionet.molbio.proteins:9500 sci.med.pharmacy:37773 bionet.molbio.embldatabank:729 bionet.population-bio:2126 bionet.molbio.evolution:5408 sci.bio.systematics:1449 bionet.software:17299 ANNOUNCEMENT AND CALL FOR PAPERS Computational Biology Session: "Computing in the Genome Era" March 31 - April 1, 1997 Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing March 31 - April 3, 1997 Georgetown University Conference Center Washington, DC, USA The Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing is scheduled to take place March 31 - April 3, 1997 at the Georgetown University Conference Center, Washington, DC, U.S.A. The objective of the Computational Biology Session "Computing in the Genome Era" (March 31 - April 1, 1997) is to discuss the current state of computational biology, its approaches, methods, general problems, achievements, and future developments with emphasis on sequence research and analysis for the Genome Projects. SPEAKERS of the session include: S. Altschul (Natl Center for Biotechnology Iinformation, Bethesda), A. Bairoch (Geneva University, Switzerland), T. Clark (Millenium Pharmaceuticals, Cambridge), W. Gish (Washington University, St. Louis), T. Gojobori (Natl Institute of Genetics, Mishima, Japan), P. Green (University of Washington, Seattle), S. Henikoff (Fred Hutchinson Cancer Research Center, Seattle), L. Hood (University of Washington, Seattle), A. Kerlavage (Institute for Genomic Research, Rockville), E. Koonin (Natl Center for Biotechnology Iinformation, Bethesda), O. Ritter (German Cancer Research Center, Heidelberg, Germany), D. Searls (SmithKline Beecham Pharmaceuticals, King of Prussia), E. Shpaer (Perkin-Elmer Applied Biosystems, Foster City), E. Trifonov (Weizmann Institute of Science, Israel). STEERING COMMITTEE: S. Altschul, A. Bairoch, W. Gish, P. Green, S. Henikoff, E. Koonin, E. Trifonov Papers (Abstracts) are invited on all relevant aspects of computational biology for presentation at the session (a new deadline is DECEMBER 23, 1996), to be selected on competitive basis by the steering committee (notification of acceptance is JANUARY 4, 1997). One-page abstracts should clearly describe the work and its conclusions. Full length manuscripts (limited to six pages) of papers presented at the conference will be published in the Conference Proceedings, in a special issue of the journal MATHEMATICAL MODELLING AND SCIENTIFIC COMPUTING, Vol. 8, 1997 (ISSN 1067-0688). The manuscripts for the special issue are due JUNE 15, 1997. The special issue of the journal will be published by SEPTEMBER 1997. ALL participants shall pay the registration fee. Abstracts (ONE PAGE, about 200 words, PLAIN JUSTIFIED TEXT) may be submitted in hard copy or via fax or by e-mail (PREFERRED) under subject "Abstract". The abstracts must be formatted to fit on 8-1/2 x 11 inch (approximately 21.5 cm x 28 cm or European Standard A-4 size) paper, typed in single space. The title must be capitalized and centered followed by the author's name(s), institution, and full address, including fax and e-mail. Send two copies (ONE copy if sent by fax or e-mail) of the abstract to the session organizer before DECEMBER 23, 1996: Eugene Kolker Dept of Molecular Biotechnology and Genome Center Box 357730, University of Washington Seattle, WA 98195-7730, USA Fax: +1-206-685-7301 E-mail: egn@u.washington.edu The Computational Biology Session is proudly sponsored by SMITHKLINE BEECHAM and MILLENIUM. You can find additional info on our Web site: http://www.genome.washington.edu/~eugene/meeting.html From owner-embldatabank@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: scistra@cs.sandia.gov (Sorin C. Istrail) Newsgroups: bionet.molbio.embldatabank Subject: RECOMB 97: Final Program, Stud Financial Support, Babysitting, Travel Date: 7 Dec 1996 02:12:28 -0000 Lines: 496 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <58ajqc$j1q@mserv1.dl.ac.uk> Original-To: embl-db@dl.ac.uk RECOMB97 NEWS December 6, 1996 **************** recomb97@hto.usc.edu http://www.cs.sandia.gov/recomb97 http://www.eldoradohotel.com Reminder: Early registration deadline (extended to Dec 20, 1996) is approaching fast!! THE ELDORADO HOTEL IS FULL!!! However, there are a few extra rooms available at the RECOMB 97 rate. Please hurry up. The overflow will go to the Hilton of Santa Fe Hotel (1-800-336-3676 or fax 505-986-6439 ask for the "RECOMB97 Conference") where we have a block of rooms reserved at identical rates. 1. RECOMB'97 Final Program 2. Available Financial support for students/graduate students/postdocs. Thanks to the generous help from the Sloan Foundation and the U.S. Department of Energy. 3. Babysitting and Recreational Activities 4. Travel to Santa Fe --------------------------------------------------------- 1. RECOMB'97 Final Program FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY 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 RECOMB 97 SCHEDULE ****************** *************************************** Sunday January 19, 1996 *************************************** 7:00-10:00 p.m. Reception Eldorado Hotel Anasazi South *************************************** Monday January 20, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom 8:45 a.m. Opening Remarks: Michael Waterman, General RECOMB Chair 1997 Program Committee Chair Sorin Istrail, General RECOMB Vice-Chair 1997 Conference Chair Pavel Pevzner, General RECOMB Chair 1998 Program Committee Chair --------------------------------------- 9:00 Distinguished Conference Lecture Session Pavel Pevzner, Chair Rich Roberts Hunting for new restriction enzymes in GeneBank --------------------------------------- 10:00 Break Session on Mapping Chair: Phil Green 10:15 Shili Lin, Terence P. Speed An Algorithm for Haplotype Analysis 10:40 Donna Slonim, L. Kruglyak, L. Stein, E. Lander Building Human Genome Maps with Radiation Hybrids Break 11:05 Session on Genomic Rearrangements Chair: Richard Karp 11:15 Haim Kaplan, Ron Shamir, Robert Tarjan Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals 11:40 David Sankoff, V. Ferretti, Joe Nadeau Conserved segment identification 12:05 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Pavel Pevzner, Chair Rob Lipshutz DNA Probe Arrays - Accessing the Genome --------------------------------------- 2:30 Break Session on New Technologies Chair: Gene Myers 2:45 J. Richard Bradley, Steven Skiena Fabricating Arrays of Strings 3:10 Dan Fasulo, Tao Jiang, Richard M. Karp, R. Settergren, E. C. Thayer An Algorithmic Approach to Multiple Complete Digest Mapping 3:45 S. Muthukrishnan, Laxmi Parida A highly effective simple combinatorial approach for constructing physical maps by optical mapping 4:10 Break --------------------------------------- 4:25 Invited Lecture Session Sam Karlin, Chair Terry Speed Variations on a theme of Lander and Waterman --------------------------------------- 8:00-10:00 p.m. Business Meeting, Anasazi Ballroom *************************************** Tuesday January 21, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom --------------------------------------- 8:30 Invited Lecture Session Rich Roberts, Chair David Botstein Expression Arrays: An Open Problem for Mathematicians in Post-Genome Sequence Biology --------------------------------------- 9:30 Break Session on Sequence Alignment Chair: Steven Altschul 9:45 Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller Progressive Multiple Alignment with Constrains 10:10 George A. Komatsoulis, Michael Waterman Chimeric alignment by dynamic programming: Algorithm and biological uses 10:35 Break Session on Sequence Alignment Chair: Temple Smith 10:45 Gary Benson Sequence Alignment with Tandem Duplication 11:10 K. Reinert, Hans-Peter Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu A Branch-and-Cut Algorithm for Multiple Sequence Alignment 11:35 Ralf Zimmer, Tom Lengauer Fast and Numerically Stable Parametric Alignment of Biosequences 12:00 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Mike Waterman, Chair Sam Karlin Assesing Inhomogeneities in Bacterial Long Genomic Sequences --------------------------------------- 2:30 Break Session on Gene Recognition Chair: Gary Stormo 2:45 Ying Xu, Edward Uberbacher Reference-based Gene Model Prediction on DNA Contigs 3:10 Sing-Hoi Sze, Pavel Pevzner Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment 3:35 Break Session on Protein Folding Chair: Martin Karplus 3:45 Ken Dill, Andrew T. Phillips, J. Ben Rosen, Protein Structure Prediction and Potential Energy Landscape Analysis using Continuous Global Minimization 4:10 William Hart, S. Istrail Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal 4:10 Break --------------------------------------- 4:25 Invited Lecture Session Martin Karplus, Chair Temple Smith The threading approach to the inverse protein folding problem --------------------------------------- 7:00 p.m. Cocktails, Anasazi Ballroom 7:30-10:00 Banquet, Anasazi Ballroom --------------------------------------- 7:30 Stanislaw Ulam Computational Biology Address Session Mike Waterman, Chair Eric Lander The Human Genome and Beyond --------------------------------------- *************************************** Wednesday January 22, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom --------------------------------------- 8:30 Invited Lecture Session Sorin Istrail, Chair Martin Karplus Protein Dynamics: From the Native to the Unfolded State and Back Again --------------------------------------- 9:30 Break Session on Protein Folding Chair: Bonnie Berger 9:45 William Hart On the Computational Complexity of Sequence Design Problems 10:10 Tatsuya Akutsu, S. Miyano On the Approximation of Protein Threading 10:45 Break Session on Mapping Chair: Ron Shamir 10:55 Amir Ben-Dor, Benny Chor On Constructing Radiation Hybrid Maps 11:20 Fengzhu Sun, Gary Benson, Mike Waterman Pooling Strategies for Establishing Physical Genome Maps Using FISH 11:45 Mutida Jain, Gene Myers Algorithm for Computing and Integrating Physical Maps Using Unique Probes 12:10 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Sorin Istrail, Chair Jonathan King Problems in Understanding the Structure and Assembly of Viruses --------------------------------------- 2:30 Break Session on Protein Folding Chair: Bonnie Berger 2:45 Richa Agarwala, Serafim Batzogloa, V. Dancik, Scott E. Decatur, M. Farach, S. Hannenhalli, S. Muthukrishnan, S. Skiena Local Rules for Protein Folding on Triangular Lattice and generalized Hydrophobicity in the HP Model 3:10 Hans-Peter Lenhof New Contact Measures for the Protein Docking Problem 3:35 Break Session on Proteins Chair: Thomas Lengauer 3:45 Bonnie Berger, Mona Singh An Iterative Method for Improved Protein Structural Motif Recognition 4:10 Erich Bornberg-Bauer Chain Growth Algorithms for HP-Type Lattice Proteins 4:35 Hiroshi Mamitsuka Supervised Learning of Hidden Markov Models for Sequence Discrimination *************************************** Thursday January 23, 1996 *************************************** General Session, Sweeney Convention Center Session on Sequence Alignment Chair: Martin Farach 8:30 Zheng Zhang, William R. Pearson, Webb Miller Aligning a DNA Sequence with a Protein Sequence 8:55 Eric L. Anson, Gene Myers ReAligner: A Program for Refining DNA Sequence Multi-Alignments 9:20 Lusheng Wang, Tao Jiang, Dan Gasfield A More Efficient Approximation Scheme for Tree Alignment 9:20 Break Session on Genomic Rearrangements Chair: David Sankoff 9:35 B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweekyk On the Complexity and Approximation of Syntenic Distance 10:00 Alberto Caprara Sorting by Reversals is Difficult 10:25 Break Session on Statistics Chair: Bruce Weir 10:40 Simon Heath The application of Markov Monte Carlo Methods to Radiation Hybrid Mapping 11:05 M. G. Reese, F. H. Eeckman, D. Kulp, D. Haussler Improved Splice Site Detection in Genie 11:30 Gary A. Churchill Monte Carlo Sequence Alignment 11:55 Lunch, Sweeney Convention Center Session on Sequence Alignment Chair: Webb Miller 1:30 Benno Schwikowski, Martin Vingron The Deferred Path Heuristic for the Generalized Tree Alignment Problem 1:55 Tetsuo Shibuya, Hiroshi Imai New Flexible Approaches for Multiple Sequence Alignment 1:55 Break Session on Mapping Chair: Maynard Olson 2:05 T. Christof, M. J\"unger, John Kececioglu, P. Mutzel, G. Reinel A Branch-and-cut Approach to physical mapping with end-probes 2:30 David Wilson, David Greenberg, Cynthia Phillips Beyond Islands: Runs in Clone-Probe Matrices 2:55 Break Session on Evolutionary Trees and DNA Computing Chair: Martin Vingron 3:05 Jamie Cohen, Martin Farach Numerical Taxonomy on Data: Experimental Results 3:30 W. Cai, Anne Condon, R.Mm Corn, E Glasser, Z. Fei, T. Frutos, Z. Guo, MG Lagally, Q. Lui, L.M. Smith, A. Theil The Power of Surface-Based DNA Computing 3:55 M. Ogihara, A. Ray Simulating Boolean Circuits on a DNA Computer End of RECOMB 97 -------------------------------------------------- 2. Financial support for students/graduate students/postdocs Limited support for students is available. We anticipate being able to make about 22 financial awards of $400 each for 22 students. Please send us a one-page request to via email to scistra@cs.sandia.gov including your affiliation, the name of your Ph.D. adviser (if appropriate) and the area of research that you are working on. We would like to select for support the students that will benefit the most from our meeting as well as those that will be able to make valuable contributions to the conference. 3. Babysitting and Recreational Activities "Santa Fe Destinations" is a company located in the Eldorado Hotel. They provide professional services for: babysitting, airport transportation, entertainment, recreational activities, spouse programs etc. Please call Tom Williams the Director of the company for services related to your visit in Santa Fe. 4. Travel to Santa Fe http://www.eldoradohotel.com/getting_there.html By plane to the Albuquerque International Airport. All major airlines use the airport. From there "Shuttlejack" ((505) 988-2441; $20 one-way trip; about one hour long) buses pick people up and drop them directly at the Eldorado Hotel nine times a day. Please call Shuttlejack and make reservations. The complete information about arriving at the Eldorado Hotel is available from their web page http://www.eldoradohotel.com/getting_there.html We hope to see you soon in Santa Fe. -- Sorin Istrail Conference Chair From owner-embldatabank@net.bio.net Mon Dec 16 22:00:00 1996 Newsgroups: embnet.general,bionet.molbio.embldatabank Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!newspump.sol.net!howland.erols.net!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: EMBL Release 49 available Sender: news@ebi.ac.uk (usenet news) Message-ID: <1996Dec16.182152@ebi.ac.uk> Date: Mon, 16 Dec 1996 18:21:52 GMT Lines: 20 Organization: European BioInformatics Institute Release 49 (December 1996) of the EMBL Nucleotide Sequence Database is available from the EBI anonymous FTP server: ftp.ebi.ac.uk/pub/databases/embl/release There is one new database file HTG.DAT containing 'High Throughput Genome Sequences'. A new taxonomy in common with NCBI-GenBank has been implemented. This release contains 1,047,263 sequences, 696,183,789 bases, an increase of about 14% over release 48. More details are in the release notes available at URLs: ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.doc http://www.ebi.ac.uk/ebi_docs/embl_db/relnotes49/relnotes.html For those who download our file of cumulative updates (cumulative.dat.Z), please note that this file will change (become smaller) on 18.12.96 at 15:00 to contain only data created since release 49. Regards, Peter Stoehr EMBL-EBI From owner-embldatabank@net.bio.net Fri Dec 20 22:00:00 1996 Path: biosci!biosci!not-for-mail From: malik@uranus.ebi.ac.uk (Ansar Malik) Newsgroups: bionet.immunology,bionet.molbio.embldatabank,bionet.software.srs Subject: ANNOUNCEMENT: Immunogenetics IMGT database - update Date: 21 Dec 1996 13:45:31 -0800 Organization: European Bioinformatics Institute (EMBL) - UK Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: malik@uranus.ebi.ac.uk (Ansar Malik) NNTP-Posting-Host: net.bio.net Keywords: database, immunogenetics, immunoglobulin, T cell receptor cell,sequences annotation, DNA sequence Xref: biosci bionet.immunology:10503 bionet.molbio.embldatabank:738 bionet.software.srs:383 IMMUNOGENETICS IMGT DATABASE =================================== Professor Marie-Paule LEFRANC Laboratoire d'ImmunoGenetique Moleculaire, LIGM UMR CNRS 9942, Institut de Genetique Moleculaire BP 5051, 1919 route de Mende, 34033 MONTPELLIER Cedex 1 FRANCE Telephone: (33) 67 61 36 34 FAX : (33) 67 04 02 31/67 04 02 45 e-mail : lefranc@ligm.crbm.cnrs-mop.fr INTRODUCTION ============ The ImMunoGeneTics database, IMGT, is an integrated specialised database containing nucleotide sequence information of genes important in the function of the immune system. It collects and annotates sequences belonging to the immunoglobulin superfamily which are involved in immune recognition, these are the B cell antigen receptor (Immunoglobulin or Ig), the T cell antigen receptor (TCR) (LIGM-database) and the class I and class II molecules of the Human Leucocyte Antigens (HLA) system (HLA-database). IMGT/LIGM DATABASE ================== An integrated immumogenetics database (IMGT/LIGM) specialising in Ig and TcR is under development through collaboration between LIGM, IFG and EMBL oustation EBI. This database consists of the Ig and TcR sequence entries. Collaborators: Release 96.11 contains 7937 fully annotated sequence entries. LIGM Montpellier :Marie-Paule Lefranc (coordinator) Veronique Giudicelli,Denys Chaume EMBL-EBI :Ansar Malik IFG :Werner Mueller ACCESS/DATA DISTRIBUTION ======================== SRS server: http://www.ebi/srs/srsc NOTE: Selecting this option will bring you to the SRS qerry interface page, where you have to select "search Sequence Libraries" WWW server: http://www.ebi.ac.uk/imgt/ FTP server: ftp.ebi.ac.uk/pub/databases/imgt E_MAIL server: email netserv@ebi.ac.uk -- send "help IMGT" in the mail body. This database is available on CD-ROM as an acompanying database to the EMBL Nucleotide Sequence Database at nominal cost. ======================================================================= Ansar Malik Ph.D | Email:Malik@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (1223) 494417 Cambridge CB10 1RQ, UK | Fax: +44 (1223) 494968 ======================================================================== From owner-embldatabank@net.bio.net Fri Dec 27 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in1.uu.net!205.164.220.8!news.monmouth.com!news From: egrimaldi@monmouth.com (Edward Grimaldi) Newsgroups: bionet.molbio.embldatabank Subject: GET RID OF CREDIT CARD DEBT!!!! Date: Fri, 27 Dec 1996 23:12:45 GMT Organization: Monmouth Internet Lines: 55 Message-ID: <5a1lev$dpl@news.monmouth.com> NNTP-Posting-Host: sl-ppp27.monmouth.com X-Newsreader: Forte Free Agent 1.0.82 GET RID OF CREDIT CARD DEBT!!!! Have you got yourself into a situation that seems hopeless? Does it feel as though you'll be paying off your credit cards forever without reducing the balances? There is a solution you can try for FREE!!!! Download for FREE, a fully functional version of..... * * * * * Credit Card Counselor 1.0 * * * * * ** Reach a point where you have no credit card bills! ** Stop paying high interest payments that get you nothing! ** Free up the lines of credit you'll need for emergencies! This simple and versatile windows95 application can help you create a realistic budget that you can live with. Develop a strategy plan designed to eliminating credit card debt forever! Don't go Bankrupt! Don't develop bad credit! Pay your bills responsibly and consistently on a reasonable and simple monthly budget plan that you help to design! The program can be downloaded for FREE at... http://www.shopucc.com/credit.html It's shareware, so you can try it first! If you like it, go ahead and register it! This simple module ** Maintains credit card information, ** calculates interest, ** calculates and suggests payment amounts, ** determines how long it will take to pay off your debt, ** tells how much money per month is needed to pay things off within a time frame that YOU ESTABLISH!!! 3 MONTHS - 6 MONTHS - 12 MONTHS - 18 MONTHS - 24 MONTHS The objective of our program is to help you set achievable goals. Aim at eliminating all your credit card obligations in a way that preserves your credit rating and gives you piece of mind. DOWNLOAD IT RIGHT NOW FOR FREE!!!!!!! http://www.shopucc.com/credit.html From owner-embldatabank@net.bio.net Tue Dec 31 22:00:00 1996 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!howland.erols.net!cliffs.rs.itd.umich.edu!newsxfer2.itd.umich.edu!uunet!in1.uu.net!192.35.48.11!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: Sprot32.dat/ prosite13.2 X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.3/Emacs 19.34 Distribution: bionet Date: Wed, 1 Jan 1997 16:49:12 GMT Lines: 13 I need a consistent prosite/swiss-prot pair of databases to build an annotated database. This could either provided by finding: sprot32.dat, which works with the widely available prosite rel. 13. Or prosite rel. 13.2, which is consistent with the current sprot34.dat. Unfortunately, I cannot find it anywhere. Bill Pearson