From BIOSCI-REQUEST Tue Oct 1 16:55:15 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id QAA01903; Tue, 1 Oct 1996 16:55:15 -0700 Received: from spidergram.ccs.unr.edu (spidergram.comnet.unr.edu [134.197.75.15]) by net.bio.net (8.6.12/8.6.6) with ESMTP id QAA01891; Tue, 1 Oct 1996 16:54:58 -0700 Received: from earth.ers.unr.edu by spidergram.ccs.unr.edu (8.7.6/1.34) id QAA07445; Tue, 1 Oct 1996 16:54:43 -0700 ( ) Received: from earth.ers.unr.edu by earth.ers.unr.edu (8.7.5/1.34-UNR-sd-ptp-1.00) id XAA24719; Tue, 1 Oct 1996 23:53:42 GMT Date: Tue, 1 Oct 1996 16:53:42 -0700 (PDT) From: James Lyons-Weiler To: rna@net.bio.net cc: dinosaur@lepomis.psych.upenn.edu, roots-l@vm1.nodak.edu, mollusca@ucmp1.berkeley.edu Subject: Free Phylogenetics Software - RASA 2.0 (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII (Apologies for semi-redundant or cross postings) Date of Upgrade: October 1, 1996 ********************************************************************* *********************** Announcing RASA 2.0 ************************* ********************************************************************* Software for the Mac that will perform "Relative Apparent Synapomorphy Analysis" (RASA) has been updated and is freely available at the address below. RASA is a statistical test for the presence of phylogenetic signal (a.k.a. cladistic hierarchy) in _any_ type of discrete character data matrix (morphological/molecular/combined). RASA belongs to the family of inferential statistics, which focuses on hypothesis testing. Functionally, the test compares the observed and null rates of increase in cladistic similarity among pairs of taxa predicted by an increase in the phenetic similarity among taxon pairs. The test statistic follows Student's t distribution (cf., a t-test). The software (updated from 1.1.1 to 2.0) is now available FREE at the following URL as a binhexed self-extracting archive: http://loco.biology.unr.edu/archives/rasa/rasa.html and by anonymous ftp at loco.biology.unr.edu (pub) (rasa) There you'll find rasa.sea, which contains the following: RASA 2.0 <-- Reads a data file, measures signal, reports the result in tabular form, AND allows you to plot and explore the RASA regression. RASA 2.0 replaces RASA 1.1.1 and RASA Plot 1.1.1. sample.data <-- A sample data file with signal. README-2.0 <-- A file with FAQs, bugs, etc. SoftwareFPU <-- Allows FPU machines to run RASA 2.0. PLUS LINKS to other Phylogenetic Information on the Web. **** CHANGES IN 2.0 **** RASA 2.0 is much more sophisticated and user friendly than 1.1.1: User interface Menu-driven analyses Menu-driven graphics Identify specific taxa in the RASA regression (RASA Plot is now incorporated into 2.0) Data entry No more COMMAS between characters! See new sample data file for data entry format Data analysis Multiple outgroups can be defined. Planned Upgrades Printing capability will be added. Including/Excluding Taxa will be added. New analytical tools for phylogenetic data exploration based on the RASA test will be implemented _after_ they have survived peer review. RASA 2.0 will be upgraded after each analysis is implemented. Check for upgrades monthly. The reference for the algorithm and detailed justification and discussion of limitations of the approach can be found in: Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. 1996. Relative Apparent Synapomorphy Analysis (RASA) I: the statistical measurement of phylogenetic signal. Molecular Biology and Evolution 13:749-757. Send questions off the list; FAQs will be included in the README file as they arrive. To add your name to the RASA mailing list, or if you have questions, send an email with your postal to weiler@ers.unr.edu James Lyons-Weiler Ecology, Evolution, and Conservation Biology 1000 Valley Road/186 University of Nevada, Reno Reno, NV 89512 From BIOSCI-REQUEST Wed Oct 9 02:00:20 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id CAA24229; Wed, 9 Oct 1996 02:00:20 -0700 Received: (from biohelp@localhost) by net.bio.net (8.6.12/8.6.6) id CAA24204; Wed, 9 Oct 1996 02:00:09 -0700 Date: Wed, 9 Oct 1996 02:00:09 -0700 From: BIOSCI Administrator Message-Id: <199610090900.CAA24204@net.bio.net> To: rna@net.bio.net Subject: BIOSCI/bionet miniFAQ & Fundraiser (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 BIOSCI-REQUEST Tue Oct 15 09:27:08 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id JAA12182; Tue, 15 Oct 1996 09:27:08 -0700 Received: from iunsun2 (iunsun2.iun.indiana.edu [149.162.1.7]) by net.bio.net (8.6.12/8.6.6) with SMTP id JAA12156; Tue, 15 Oct 1996 09:26:47 -0700 Received: from iunhaw1.iun.indiana.edu by iunsun2 (5.x/ardent-1.0/jsm) id AA07736; Tue, 15 Oct 1996 11:27:10 -0500 Received: from IUNHAW1/MERCURY_Q1 by iunhaw1.iun.indiana.edu (Mercury 1.21); 15 Oct 96 11:27:31 CST Received: from MERCURY_Q1 by IUNHAW1 (Mercury 1.21); 15 Oct 96 11:27:29 CST From: "Tim Stabler" Organization: Indiana University Northwest To: rna@net.bio.net Date: Tue, 15 Oct 1996 11:27:22 CST Subject: Re: Meeting Reply-To: tstabler@iunhaw1.iun.indiana.edu Priority: normal X-Mailer: Pegasus Mail v3.22 Message-Id: <4EAC006F7@iunhaw1.iun.indiana.edu> I would like to announce that next year, June 14-18, the Society for In Vitro Biology will be holding its Congrtess at the Renaissance Hotel in Washington, D.C. Various symposia and workshops are planned, some of which directly interface with this group. If you would like further information, please Email me your snail- mail address and I will get it to you immediately. Or, if you are into the Web, you can look up "SIVB" on your net search. Especially, if you are using Netscape Navigator and the "Infoseek" area. There you will find all sorts of information about the group, past meetings and plans for this meeting. If you wish, you might be able to be a poster presenter or speaker. I can get you that information also. There will be an exhibit area from various companies. If you Email me, please note that in my address it is "iunhaw(one)" and not an "L" there. I have had several folks make this mistake. Thanks for you time. Timothy A. Stabler, Ph.D. Department of Biology Indiana University Northwest Gary, IN 46408 (219)980-6718 FAX: (219)980-7125 Timothy A. Stabler, Ph.D. Department of Biology Indiana University Northwest Gary, IN 46408 (219)980-6718 FAX: (219)980-7125 From BIOSCI-REQUEST Tue Oct 15 20:37:43 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id UAA25467; Tue, 15 Oct 1996 20:37:43 -0700 Received: from huon.itd.adelaide.edu.au (root@huon.itd.adelaide.edu.au [129.127.40.3]) by net.bio.net (8.6.12/8.6.6) with SMTP id UAA25462; Tue, 15 Oct 1996 20:37:24 -0700 Received: from [192.133.41.100] by huon.itd.adelaide.edu.au with SMTP (5.61+IDA+MU+NF/UA-5.28B) id AA14991; Wed, 16 Oct 1996 13:07:53 +0930 (from ggoodall@immuno.imvs.sa.gov.au for rna@net.bio.net) Received: from IMVS-IMMUNO/SpoolDir by immuno.imvs.sa.gov.au (Mercury 1.21); 16 Oct 96 13:07:13 +1030 Received: from SpoolDir by IMVS-IMMUNO (Mercury 1.21); 16 Oct 96 13:06:48 +1030 From: "GREG GOODALL" Organization: Institute of Med. & Vet. Science To: rna@net.bio.net Date: Wed, 16 Oct 1996 13:06:41 GMT+1030 Subject: post-doc position X-Confirm-Reading-To: "GREG GOODALL" X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail for Windows (v2.23) Message-Id: <766E3A5EBE@immuno.imvs.sa.gov.au> I am looking for a post-doctoral fellow to join my lab to study the function/mechanism of a newly discovered mRNA-destabilising element that is present in a number of growth factor mRNAs (PNAS, in press). Anyone interested please contact me for further information. Greg Goodall ggoodall@immuno.imvs.sa.gov.au Dr. Greg Goodall Hanson Centre for Cancer Research I.M.V.S. Frome Road Adelaide, S.A. 5000 Australia From BIOSCI-REQUEST Thu Oct 17 15:03:43 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id PAA15424; Thu, 17 Oct 1996 15:03:43 -0700 Received: from icarus.cc.uic.edu (root@ICARUS-FDDI.CC.UIC.EDU [128.248.100.53]) by net.bio.net (8.6.12/8.6.6) with ESMTP id PAA15415; Thu, 17 Oct 1996 15:03:24 -0700 Received: from [128.248.34.161] (C057.PHARM.UIC.EDU [128.248.34.161]) by icarus.cc.uic.edu (8.7.6/8.7.6) with SMTP id RAA24220 for ; Thu, 17 Oct 1996 17:04:57 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Oct 1996 17:06:40 -0600 To: rna@net.bio.net From: shura@uic.edu (Alexander Mankin (Shura)) Subject: biotinylated RNA We need an advice for introducing biotin in the RNA 3' or 5' end. We cannot use periodate chemistry and thus have to use an enzymatic approach. There is biotinylated UTP on the market. Does anyone know if terminal deoxynucleotidyl transferase will add rNTP or dNTP to the RNA 3' end? Any reference? Are there any good biotinilated substrates for RNA ligase? Would anyone have other ideas of how to biotinylate RNA end? Cheers. Alexander Mankin From BIOSCI-REQUEST Tue Oct 22 17:01:09 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id RAA07568; Tue, 22 Oct 1996 17:01:09 -0700 Received: from cs.sandia.gov (cs.sandia.gov [132.175.13.2]) by net.bio.net (8.6.12/8.6.6) with SMTP id RAA07559; Tue, 22 Oct 1996 17:00:45 -0700 Received: from frodo2.cs.sandia.gov by cs.sandia.gov with smtp (Smail3.1.28.1 #5) id m0vFqih-000XXAC; Tue, 22 Oct 96 17:58 MDT Received: by frodo2.cs.sandia.gov (SMI-8.6/SMI-SVR4) id RAA02181; Tue, 22 Oct 1996 17:56:08 -0600 Date: Tue, 22 Oct 1996 17:56:08 -0600 From: scistra@cs.sandia.gov (Sorin C. Istrail) Message-Id: <199610222356.RAA02181@frodo2.cs.sandia.gov> To: rna@net.bio.net Subject: RECOMB 97: CALL FOR POSTERS; LIST OF ACCEPTED PAPERS RECOMB 97 NEWS ************** October 22, 1996 1. REMINDER: CALL FOR POSTERS (deadline Oct 25, 96) 2. List of accepted papers to RECOMB 97 ------------------------------------------------ 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. This is a reminder that the deadline for receiving a poster abstract for RECOMB 97 is OCTOBER 25, 1996. This call is for a one page abstract. The actual space for the poseter presentation will be a regular poster space accomodating about 15 pages. Call for RECOMB 97 Posters ************************** Please send a one-page abstract of your Poster including title, authors, 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 --------------------------------------------- 2. The List of Accepted Papers for RECOMB 97: ****************************************** Name: Zheng Zhang, William R. Pearson, Webb Miller Title: Aligning a DNA Sequence with a Protein Sequence Name: Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller Title: Progressive Multiple Alignment wtih Constraints Name: Ken Dill, Andrew T. Phillips, J. Ben Rosen Title: Protein Structure Prediction and Potential Energy Landscape Analysis using Continuous Global Minimization Name: Alberto Caprara Title: Sorting by Reversals is Difficult Name: J. Richard Bradley, Steven Skiena Title: Fabricating Arrays of Strings Name: Simon Heath Title: The application of Markov Monte Carlo methods to radiation hybrid mapping Name: Tatsuya Akutsu, Satoru Miyano Title: On the Approximation of Protein Threading Name: Eric L. Anson, Gene Myers Title: ReAligner: A Program for Refining DNA Sequence Multi-Alignments Name: George A. Komatsoulis, Michael Waterman Title: Chimeric alignment by dynamic programing: Algorithm and biological uses Name: Gary A. Churchill Title: Monte Carlo Sequence Alignment Name: Benno Schwikoski, Martin Vingron Title: The Deferred Path Heuristic for the Generalized Tree Alignment Problem Name: Tao Jiang, Richard M. Karp Title: Mapping Clones with a Given Ordering or Interleaving Name: Jamie Cohen, Martin Farach Title: Numerical Taxonomy on Data: Experimental Results Name: Dan Fasulo, Tao Jiang, Richard M. Karp, R. Settergren, E. C. Thayer Title: An Algorithmic Approach to Multiple Complete Digest Mapping Name: Sing-Hoi Sze, Pavel Pevzner Title: Towards 100% Accurate Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment Name: Ralf Zimmer, Tom Lengauer Title: Fast and Numerically Stable Parametric Alignment of Biosequences Name: Tao Jiang, Lusheng Wang, Dan Gusfield Title: A More Efficient Approximation Scheme for Tree Alignment Name: Serafim Batzogloa, Scott E. Decatur Title: Constant Approximation Algorithm on the Triangular Lattice and Generalized Hydrophobicity for Protein Folding in the Hydrophobic-Polar Model Name: S. Muthukrishnan, Laxmi Parida Title: A highly effective simple combinatorial approach for constructing physical maps by optical mapping Name: Richa Agarwala, V. Dancik, S. Hannenhalli, M. Farach, S. Muthukrishnan, S. Skiena Title: Local Rules for Protein Folding on a Triangular Lattice Name: K. Reinert, Hans-Peter Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu Title: A Branch-and-Cut Algorithm for Multiple Sequence Alignment Name: Hans-Peter Lenhof Title: New Contact Measures for the Protein Docking Problem Name: Haim Kaplan, Ron Shamir, Robert Tarjan Title: Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals Name: Ying Xu, Edward Uberbacher Title: Reference-based Gene Model Prediction on DNA Contigs Name: B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweekyk Title: On the Complexity and Approximation of Syntenic Distance Name: Mutida Jain, Gene Myers Title: Algorithm for Computing and Integrating Physical Maps Using Unique Probes Name: Gary Benson Title: Sequence Alignment with Tandem Duplication Name: Hiroshi Mamitsuka Title: Supervised Learning of Hidden Markov Models for Sequence Discrimination Name: William Hart Title: On the Computational Complexity of Sequence Design Problems Name: William Hart, Sorin Istrail Title: Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86\% of Optimal Name: David Greenberg, Cynthia Phillips, David Wilson Title: Beyond Islands: Ambiguity in Random Clone-Probe Matrices Name: David Sankoff, V. Ferretti, Joe Nadeau Title: Conserved segment identification Name: John Kececioglu, T. Christof, M. J\"unger, P. Mutzel, G. Reinelt Title: A branch-and-cut approach to physical mapping with end-probes Name: Donna Slonim, L. Kruglyak, L. Stein, Eric Lander Title: Building Human Genome Maps with Radiation Hybrids Name: Bonnie Berger, Mona Singh Title: An Iterative Method for Improved Protein Structural Motif Recognition Name: Fengzhu Sun, Gary Benson, Mike Waterman Title: Pooling Strategies for Establishing Physical Genome Maps Using FISH Name: M. Ogihara, A. Ray Title: Simulating Boolean circuits on a DNA computer Name: M. G. Reese, F. H. Eeckman, D. Kulp, D. Haussler Title: Improved Splice Site Detection in Genie Name: Amir Ben-Dor, Benny Chor Title: On Constructing Hybrid Maps Name: Shili Lin, Terence P. Speed Title: An Algorithm for Haplotype Analysis Name: Tetsuo Shibuya, Hiroshi Imai Title: New Flexible Approaches for Multiple Sequence Alignment Name: Erich Bornberg-Bauer Title: Chain Growth Algorithms for HP-Type Lattice Proteins Name: W Cai, Anne Condon, RM Corn, E Glasser, Z. Fei, T. Frutos, Z. Guo, MG Lagally, Q Lui, LM Smith, A Theil Title: The Power of Surfaced-based DNA Computation ----------------------------------------- See you in Santa Fe, Mike Waterman, Pavel Pevzner and Sorin Istrail