From owner-genome-program@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: DOE HGP call for proposals Date: 2 Jul 1997 10:16:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 225 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5pe2cr$9u8@net.bio.net> NNTP-Posting-Host: net.bio.net http://www.er.doe.gov/production/grants/fr97_17.html (General instructions for applying for DOE Grants are available at: http://www.er.doe.gov/production/grants/grants.html) Notice 97-17 Human Genome Program Technologies in Support of the DOE Joint Genome Institute Department of Energy Office of Energy Research Energy Research Financial Assistance Program Notice 97-17; Human Genome Program - Technologies in Support of the DOE Joint Genome Institute AGENCY: U.S. Department of Energy ACTION: Notice inviting grant applications SUMMARY: The Office of Health and Environmental Research (OHER) of the Office of Energy Research (ER), U.S. Department of Energy (DOE), hereby announces its interest in receiving applications for support of the Human Genome Program. This Program is a coordinated multidisciplinary research effort to develop creative, innovative resources and technologies that lead to a molecular level understanding of the human genome. As one aspect of this program, the DOE is establishing a "Joint Genome Institute" (JGI) to develop a DNA sequencing factory. The JGI will oversee a central sequencing facility that will initially have parallel production lines that use shotgun and transposon-based directed sequencing approaches. This dual approach is intended to evolve into an optimized and unified sequencing strategy within two to three years. This unified strategy will take advantage of technologies and expertise at the JGI and in the broader research community. An important aspect of developing this automated facility will be the establishment of external collaborations and partnerships aimed at technology development. The JGI's genomic sequencing program will also be coupled to a collection of experimental functional genomics approaches designed to provide a partial functional characterization of the genes as they are revealed by the sequencing. Here, the primary goal will be to develop cost-effective approaches that can yield worthwhile functional information. A related goal is to develop improved ways of integrating human genomics with the information coming from model organism genomics. DATES: Preapplications referencing Program Notice 97-17 should be received by August 1, 1997. Formal applications in response to this notice must be received by 4:30 p.m., E.D.T., October 16, 1997, to be accepted for merit review and to permit timely consideration for award in FY 1998. ADDRESSES: Preapplications referencing Program Notice 97-17 should be sent to Dr. Marvin E. Frazier, Office of Health and Environmental Research, ER-72, Office of Energy Research, U.S. Department of Energy, 19901 Germantown Road, Germantown, MD 20874-1290; e-mail is acceptable for submitting preapplications using the following address: joanne.corcoran@oer.doe.gov. Formal applications referencing Program Notice 97-17 should be forwarded to: U.S. Department of Energy, Office of Energy Research, Grants and Contracts Division, ER-64, 19901 Germantown Road, Germantown, MD 20874-1290, ATTN: Program Notice 97-17. This address must be used when submitting applications by U.S. Postal Service Express Mail or any commercial mail delivery service, or when hand-carried by the applicant. An original and seven copies of the application must be submitted; however, applicants are requested not to submit multiple application copies using more than one delivery or mail service. FOR FURTHER INFORMATION CONTACT: Dr. Marvin E. Frazier, ER-72, Office of Health and Environmental Research, Office of Energy Research, U. S. Department of Energy, 19901 Germantown Road, Germantown, MD 20874-1290, telephone: (301) 903-6488, e-mail: joanne.corcoran@oer.doe.gov. SUPPLEMENTARY INFORMATION: The goal of this notice is to support technology development that serves the needs of the Department of Energy's (DOE) Joint Genome Institute (JGI). The DOE JGI is developing a high throughput DNA sequencing factory. This factory will take advantage of the complementing strengths of each of the three current DOE Genome Centers: Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL). The JGI Sequencing Factory will be physically located in proximity to LLNL and LBNL. The Scientific Director of the DOE Human Genome Program, Dr. Elbert Branscomb, is the leader of the JGI. With respect to the JGI genomic sequencing task, the specific goals are: (1) to establish a cooperative technology development project with an outside entity that will produce, within two years, an automated DNA sequencing production line based on either shotgun or directed strategies; and (2) to develop and implement technologies for automated and advanced high-throughput DNA sequencing that can be integrated into the unified sequencing production strategy that is identified and implemented at the JGI. In support of the first goal, the grantee will form a close collaboration with the JGI aimed at technology co-development and transfer for high throughput production DNA sequencing. A critical success factor for this effort will be the construction of a new, highly automated pilot DNA sequencing production line at the JGI within 6 to 9 months of the project's start. The grantee, working in conjunction with the JGI, will help build and maintain automated devices as appropriate for this pilot line (e.g., those for DNA purification, DNA sequencing, and automated finishing). It is anticipated that this pilot DNA sequencing production line may use, in significant part, technology supplied by the grantee. The second phase of the project, to be completed within two years, will be the development of a high throughput DNA sequencing production line. It is anticipated that this production line will lead current technology in automation and the minimization of human labor and will ultimately produce 100-200 Mb of finished human genomic sequence per year. It is also expected that, in close cooperation with the JGI, the grantee will use the technology being supplied to perform a significant amount of DNA sequencing on targets that support the DOE effort. This would be designed to drive the technology development and to permit modifications in technology between the pilot and production phases to be evaluated and validated under high throughput conditions. It is estimated that one major award, for a total of approximately $4 million in FY 1998, will be made. In support of the second sequencing goal, technology developments aimed at improving the constituent technologies and overall performance of the JGI DNA sequencing production line are sought. These could include: innovative instrumentation and automated systems that offer the potential for rapid, cost-effective sequencing of approximately a million bases per day; for non-gel techniques and direct imaging approaches; for development of applied genome informatics software for use in DNA sequencing and functional interpretation, including information retrieval; for user interfaces compatible with Genome Data Base (GDB), Genome Sequence DataBase (GSDB), and GenBank; and for communications, software engineering, and data management. Improved algorithms and hardware for DNA sequence annotation, including identification of homologies, regulatory sites, and protein coding regions can also be included. It is anticipated that between 2-4 awards for a total of up to $1 million could be made in FY 1998. With respect to the functional genomics and model organism goals, projects in the following program areas are solicited: 1) strategies for full-length cDNA clone generation and sequencing and for economically and accurately determining transcript lengths and types; 2) strategies for expression mapping, sub-cellular localization, and pathway tracing; 3) economical approaches for revealing single base pair polymorphisms and for characterizing their haplotypes; and 4) affordable approaches for using model organisms to systematically relate phenotype information to anonymous genes discovered in the human genome. It is anticipated that between 2-4 awards for pilot and proof-of-principle studies, for a total of up to $1 million could be made in FY 1998. Potential applicants are strongly encouraged to submit a brief preapplication that consists of two to three pages of narrative describing the research objectives and methods of accomplishment. Preapplications will be reviewed relative to the scope and research needs of the DOE Human Genome Program, as outlined in the summary paragraph and in the SUPPLEMENTARY INFORMATION. Principal investigator address, telephone number, FAX number, and e-mail address are required as part of the preapplication. A response to each preapplication discussing the potential programmatic relevance of a formal application generally will be communicated to the Principal Investigator within 21 days of receipt. ER's preapplication policy can be found on ER's Grants and Contracts Web Site at: http://www.er.doe.gov/production/grants/preapp.html. It is anticipated that approximately $6 million will be available for grant awards during FY 1998, contingent upon availability of appropriated funds. Multiple year funding of grant awards is expected, with out-year funding also contingent upon the availability of appropriated funds, progress of the research, and programmatic needs. It is expected that most awards will be from one to three years and that there will be one award for approximately $4 million per year (total costs) with the remaining 4-6 awards in the $200 thousand to $400 thousand per year (total costs) range. The dissemination of materials and research data in a timely manner is essential for progress towards the goals of the DOE Human Genome Program. OHER requires the timely sharing of resources and data. Applicants should, in their applications, discuss their plans for disseminating research data and materials which may include, where appropriate, putting cell lines, probes, sequence data, etc., into public repositories. Funds to defray the costs of disseminating materials or submitting data to repositories are allowable; however, such requests must be adequately justified. Applications will be subjected to formal merit review (peer review) and will be evaluated against the following evaluation criteria which are listed in descending order of importance codified at 10 CFR 605.10(d): 1. Scientific and/or Technical Merit of the Project; 2. Appropriateness of the Proposed Method or Approach; 3. Competency of Applicant's personnel and Adequacy of Proposed Resources; 4. Reasonableness and Appropriateness of the Proposed Budget. The evaluation will include program policy factors such as the relevance of the proposed research to the terms of the announcement and an agency's programmatic needs. Note, external peer reviewers are selected with regard to both their scientific expertise and the absence of conflict-of-interest issues. Non-federal reviewers will often be used, and submission of an application constitutes agreement that this is acceptable to the investigator(s) and the submitting institution. Information about development and submission of applications, eligibility, limitations, evaluation, selection process, and other policies and procedures may be found in the ER Application Guide for the Office of Energy Research Financial Assistance Program 10 CFR Part 605, which is available on the World Wide Web at: http://www.er.doe.gov/production/grants/grants.html. The ER, as part of its grant regulations, requires at 10 CFR 605.11(b) that a grantee funded by ER and performing research involving recombinant DNA molecules and/or organisms and viruses containing recombinant DNA molecules shall comply with the National Institutes of Health "Guidelines for Research Involving Recombinant DNA Molecules" (51 FR 16958, May 7, 1986), or such later revision of those guidelines as may be published in the Federal Register. The Catalog of Federal Domestic Assistance Number for this program is 81.049 and the solicitation control number is ERFAP 10 CFR Part 605. John Rodney Clark Associate Director for Resource Management Office of Energy Research Published in the Federal Register July 1, 1997, Vol. 62, No. 126, pages 35476-35478. From owner-genome-program@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Rolf Kocherhans Newsgroups: bionet.molbio.genome-program Subject: Free practical programs for molecular biologists !!! Date: 7 Jul 1997 13:23:34 -0700 Organization: University of Zurich Lines: 52 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5prj86$bvr@net.bio.net> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: net.bio.net I wrote a few practical and simple to use programs which facilitate your daily work in the lab such as predicting the size of DNA fragments after digestion (graphical) with restriction enzymes. I would like to make these programs accessible to a broad user group by the Internet. All programs have been tested on MacOS and Windows95. My programs are accessible over the WWW and made functional using Netscape 2.x or Internet Explorer 2.x or higher in association with a free plugin which you have to download and install first. This is what you do: - Download the Roadster plugin http://www.unizh.ch/vetvir/plugin.html) install it on your computer. - Then connect to: http://www.unizh.ch/vetvir/programs.html That's it !! These are my programs which make your live as a molecular biologist easier ! Find here a few more examples or my programs: a. Digest Preview: Enter the size(s) of your DNA fragment(s) and see their migration pattern in a virtual gel in comparison to a 1 kb ladder. b. Adapter Design: Helps to create in frame adapters in order to link incompatible DNA ends together. c. Dilution Calculator: Does all the calculations when you have to make up solutions There are many other programs such as Oligo Tm, Compatible ends etc. Please have a look, comments are welcome! Have fun Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-genome-program@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: TBLASTN of new microbial genomes from TIGR Date: 8 Jul 1997 14:41:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5puc6h$her@net.bio.net> NNTP-Posting-Host: net.bio.net ------- Forwarded Message Date: Thu, 3 Jul 1997 14:56:48 -0400 To: microbial-genomes@mailbase.ac.uk Subject: TBLASTN of new microbial genomes from TIGR Cc: blast-help@ncbi.nlm.nih.gov From: francis@ncbi.nlm.nih.gov Reply-To: francis@ncbi.nlm.nih.gov Dear microbial-genomes readers, A new BLAST service for the recently released microbial genomes from The Institute for Genomic Research (TIGR) is now available at this URL: http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-tigrbl These unfinished genomes are not yet available in GenBank or Entrez. The genomes are searchable via TBLASTN (a user's protein query vs. a 6-frame translation of the microbial DNA sequences) using the new gapped BLAST algorithm (Altschul et al., 1997, submitted). regards to all, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-genome-program@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: Latest issue of Human Genome News online Date: 8 Jul 1997 14:41:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 73 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5puc6e$hea@net.bio.net> NNTP-Posting-Host: net.bio.net Human Genome News Volume 8, Numbers 3 & 4 is up on the web at: http://www.ornl.gov/TechResources/Human_Genome/publicat/hgn/v8n3/01tocont.html Table of Contents: In This Issue... Genome News Fear of Genetic Discrimination Drives Legislative Interest Pending Legislation Could Impact Research Rapid Sequencing of Microbial Genomes Opens Door to Functional Genomics Conference on Small Genomes Held at Hilton Head President's Bill Would Prohibit Human Cloning NCHGR Becomes NIH Institute Chromosome X Map Completed HUGO Calls for Patent Policy Changes Homologs of Human Disease Genes Found in Model Organisms Whitehead-MIT Teams With Consortium Merck Genomics Institute Established Notice to DOE Contractors, Grantees Web Sites NCI Cancer Gene Web Site Set to Debut The Gene Letter Available Online CBIL Web Site Web Resources HGMIS Web Sites Win Awards E-Mail Notification of HGN Web Version Available Funding Microbial Resources MAGPIE: Data on Gene Sequences Microbial Database at TIGR Complete Microbial Genome Clones Information Resources Yeast Genome Directory Published Mapping Panel Available from Coriell Stanford Center's High-Resolution Map FlyBase Updated ProDom Release 34.1 TIGR Gene Index National Flow Cytometry Resource Newsletter Special Gene Patenting issue of Bulletin of Medical Ethics Special JAMWA Genetics Issue Genetic Testing Report BSCS Genome Educational Modules AAAS Book: Exploring Public Policy Issues in Genetics Booklet on Genetics: Your Genes, Your Choices: Exploring the Issues Raised by Genetic Research Genetics Networks by Geographic Region Aid Consumers Calendars and Subscriptions Sponsors of Genome Related Training Subscriptions; Selected Acronyms From owner-genome-program@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "E. Kolker" Newsgroups: bionet.molbio.genome-program Subject: Call for papers: Recomb 98 Date: 8 Jul 1997 14:41:33 -0700 Organization: University of Washington Lines: 198 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5puc6e$he1@net.bio.net> NNTP-Posting-Host: net.bio.net CALL FOR PAPERS SECOND ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 98) March 22 - 25, 1998 New York City Sponsored by Association for Computing Machinery SIGACT with support from SLOAN Foundation US Department of Energy http://www.mssm.edu/biomath/recomb98.html The Second Annual Conference on Research in Computational Molecular Biology (RECOMB 98),sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, and US Department of Energy will be held in New York City, March 22 - 25, 1998. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Pavel Pevzner RECOMB 98 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by October 20, 1997. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 98. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 15, 1997. A final copy of each accepted paper is required by January 10, 1997. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. Conference Events RECOMB 98 will feature 8 invited lectures (to be announced later) by prominent biologists including the following conference events: THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS. The Stanislaw Ulam Memorial Lecture awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. THE DISTINGUISHED CONFERENCE LECTURE. The conference will start with the Distinguished Conference Lecture awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE. A lecture describing emerging, new technologies. BEST PAPER BY A YOUNG SCIENTIST AWARD. This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 2 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. STEERING COMMITTEE: Sorin Istrail, RECOMB General Vice-Chair (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California) PROGRAM COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson (Mount Sinai School of Medicine) Bonnie Berger (MIT) Martin Farach (Rutgers University) Phil Green (University of Washington) Dan Gusfield (University of California, Davis) David Haussler (University of California, Santa Cruz) Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Minoru Kanehisa (Kyoto University, Japan) Eugene Koonin (National Center for Biotechnology Information) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Pavel Pevzner, Program Committee Chair (University of Southern California) David Searls (SmithKline Beecham) Ron Shamir (Tel-Aviv University, Israel) Terry Speed (University of California, Berkeley) Martin Vingron (German Cancer Center) Michael Waterman (University of Southern California) ORGANIZING COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson, Conference Chair (Mount Sinai School of Medicine) Martin Farach (Rutgers University) Eugene Kolker, Publicity Chair (University of Washington) Information about local arrangements can be obtained by consulting the conference web page http://www.mssm.edu/biomath/recomb98.html or from the Conference Chair: Professor Gary Benson Department of Biomathematical Sciences Box 1023 The Mount Sinai Medical Center One Gustave L. Levy Place New York, NY 10029-6574 (212) 241-5777 phone (212) 860-4630 fax benson@ecology.biomath.mssm.edu From owner-genome-program@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: aoki@faerie.CS.Berkeley.EDU (Paul M. Aoki) Newsgroups: bionet.molbio.genome-program Subject: US-funded work in disk-based search structures Date: 8 Jul 1997 14:41:37 -0700 Organization: University of California at Berkeley Lines: 23 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5puc6h$heo@net.bio.net> Reply-To: aoki@CS.Berkeley.EDU (Paul M. Aoki) NNTP-Posting-Host: net.bio.net apologies for the fact that this is only partially on-topic. however, i suspect the people who might know the answer to this question read this group. i have a recollection that one of the major US government players (NIH?) funded a specific research program in "similarity search access methods" (disk-based search structures) a few years ago (1991?). unlike much of the current computer science work in this area, which seems to focus on suffix tree variants, this work resembled a disk-based version of FASTA (k-tuples hashed into disk buckets). i also seem to recall that it resulted in a MS thesis, but i don't remember a publication. i seem to have (uncharacteristically) lost my reference for this work, and i am having a hard time tracking it down in BIOSIS Previews (perhaps because it was not published). any pointers would be greatly appreciated! -- Paul M. Aoki | University of California at Berkeley aoki@CS.Berkeley.EDU | Dept. of EECS, Computer Science Division #1776 | Berkeley, CA 94720-1776 From owner-genome-program@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "Dr. Thomas Heinemeyer" Newsgroups: bionet.molbio.genome-program Subject: TRANSFAC 3.2 Date: 8 Jul 1997 14:41:33 -0700 Organization: Ges. f. Biotechn. Forsch. mbH (non profit) Lines: 88 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5puc6e$he3@net.bio.net> NNTP-Posting-Host: net.bio.net TRANSFAC 3.2 is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzold's SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several sequence analysis tools such as - PatSearch, which uses the sequence information contained in the SITE table for analysis of submitted sequences, - MatInspector, using a library of matrices selected from the TRANSFAC MATRIX table (see Quandt et al., Nucleic Acids Res. 23:4878-4884, 1995). Moreover, the TRANSFAC server provides a new program (SaGa: structural analysis with genetic algorithms, developed by Stefan Meier) which can be used to identify structural characteristics in the environment of aligned functional sites, e.g., transcription factor binding sites. SaGa uses a library of structural parameters developed by H. Sklenar and coworkers (MDC, Berlin; see Karas et al., CABIOS 12:441-446, 1996). The SRS5 system implemented on the TRANSFAC server comprises the following databases, in addition to the TRANSFAC tables: EMBL, EMBLNEW SWISSPROT, SWISSNEW TREMBL REMTREMBL SPTREMBL PIR EPD PDB PROSITE ENZYME EMBLNEW is now updated daily on the TRANSFAC SRS-Site with the new files from European Bioinformatics Institute (EBI) in Hinxton. Edgar Wingender Thomas Heinemeyer -- Dr. Thomas Heinemeyer Tel.: ++49(0)531 6181 295 Ges. f. Biotechn. Forsch. mbH Fax: ++49(0)531 6181 266 Abt. Genomanalyse E-Mail: thh@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/Staff/thh.html D-38124 Braunschweig From owner-genome-program@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!biosci!not-for-mail From: eddy@wol.wustl.edu (Sean Eddy) Newsgroups: bionet.molbio.genome-program Subject: Re: US-funded work in disk-based search structures Date: 9 Jul 1997 12:36:01 -0700 Organization: Washington University in St. Louis Lines: 21 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5q0p71$9cj@net.bio.net> NNTP-Posting-Host: net.bio.net In article <5puc6h$heo@net.bio.net> aoki@faerie.CS.Berkeley.EDU (Paul M. Aoki) writes: >i have a recollection that one of the major US government players >(NIH?) funded a specific research program in "similarity search access >methods" (disk-based search structures) a few years ago (1991?). >unlike much of the current computer science work in this area, which >seems to focus on suffix tree variants, this work resembled a >disk-based version of FASTA (k-tuples hashed into disk buckets). i >also seem to recall that it resulted in a MS thesis, but i don't >remember a publication. Sounds reminiscent of IBM's `FLASH' algorithm, perhaps? -- - Sean Eddy, Ph.D. - Dept. of Genetics, Washington University School of Medicine - 660 S. Euclid Box 8232, St. Louis MO 63110, USA - mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy From owner-genome-program@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: Workshop on Constraints and Bioinformatics/Biocomputing CP97 Date: 14 Jul 1997 14:25:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 124 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5qe5g2$gjt@net.bio.net> NNTP-Posting-Host: net.bio.net From: David Gilbert Subject: Workshop on Constraints and Bioinformatics/Biocomputing CP97 (CFP) Date: 10 Jul 1997 12:16:03 -0700 ---------------------------------------------------------------------------- CALL FOR PAPERS CP97 Workshop on [Image] Workshop on Constraints and Bioinformatics/Biocomputing Schloss Hagenberg, Austria November 1, 1997 ---------------------------------------------------------------------------- The workshop will be held in conjunction with the Third International Conference on Principles and Practice of Constraint Programming (CP97), October 29 - November 1, 1997 SCOPE OF THE WORKSHOP Bioinformatics is the development and application of methods in informatics for approaching problems in molecular biology, whereas Biocomputing uses naturally occurring architectures and behaviours as models for computational methods, for example neural networks, genetic algorithms, genetic programming and DNA computing. We believe that constraint programming technologies can play a very significant role in these fast developing areas. This workshop solicits contributions from researchers working in any of these exciting fields. Topics include (but are not restricted to) the application of constraint technology to * sequencing and sequence analysis * languages for the description of biomolecular structures (primary, secondary and tertiary) * description of sequences and patterns in biomolecular databases * algorithms for locating structures in biomolecular databases * discovery and data mining of biostructures * neural networks * genetic algorithms * genetic programs * DNA computing * Protein folding problems Papers that combine theory and practice are especially welcome. PAPER SUBMISSIONS Submission deadline is 15 August 1997. Authors are invited to submit original papers written in English and approximately 10 A4 pages to David Gilbert at the contact address below. We encourage authors to submit by electronic mail in self-contained Postscript format. Alternatively five paper copies may be submitted. Decisions on acceptance will be sent to authors by by 15 September 1997. PUBLICATION An informal proceedings of the workshop will be available to the workshop participants. Final copies will be due by 1 October 1997. It is expected that selected papers will be published by Springer-Verlag. ORGANISATION David Gilbert and Herbert Wiklicky Department of Computer Science City University Northampton Square London EC1V 0HB, UK drg@cs.city.ac.uk herbert@cs.city.ac.uk Ingvar Eidhammer University of Bergen Department of informatics HIB N-5020 Bergen, Norway ingvar@ii.uib.no Mark Wallace IC-Parc, William Penney Laboratory, Imperial College, London SW7 2AZ, UK. mgw@doc.ic.ac.uk Roland Yap Dept. of Information Systems & Computer Science National University of Singapore Lower Kent Ridge Road Singapore 119260 ryap@iscs.nus.sg Rolf Backofen Institut fuer Informatik/ Lehr- und Forschungseinheit fuer Theoretische Informatik (Prof. Clote) Ludwig-Maximilians-Universitaet Muenchen Oettingenstrasse 67 D-80538 Muenchen, Germany backofen@informatik.uni-muenchen.de IMPORTANT DATES 15 August 1997: Paper submissions 15 September 1997: Acceptance decisions 10 October 1997: Final copy due 1 November 1997: Workshop FURTHER INFORMATION Additional information will be available at the CP97 web site: http://www.mpi-sb.mpg.de/conferences/CP97/ ------- End of Forwarded Message ------- End of Forwarded Message From owner-genome-program@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: NAS Colloquium announcement Date: 14 Jul 1997 14:25:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 153 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5qe5g6$glr@net.bio.net> NNTP-Posting-Host: net.bio.net From: mpotter@chemcca11.ucsd.edu (Michael Potter) Subject: NAS Colloquium announcement Date: 10 Jul 1997 12:03:48 -0700 *************************************************************************** NATIONAL ACADEMY OF SCIENCES COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE 11-13 September 1997 Beckman Center of the National Academies of Sciences and Engineering Irvine, California Dear Colleague, We are pleased to invite you to attend the NAS "Colloquium on Computational Biomolecular Science," to be held in Irvine, California, September 11-13, 1997. The Colloquium is intended to stimulate interdisciplinary discussion across the areas of biomolecular structure, function, and evolution, and to point to ways in which computation can help to explore the interfaces among these areas. Attendance will be limited to about 200 participants. A diverse group of speakers will provide points of departure for the discussion, but ample time will be allowed for general and informal elaboration. The speakers will include Peer Bork (EMBL, Heidelberg) Wen-Hsiung Li (Univ. Texas, Houston) Douglas Brutlag (Stanford) Alexey Murzin (MRC, Cambridge) William Eaton (NIH) Jose Onuchic (UCSD) Ron Elber (Hebrew Univ) Gregory Petsko (Brandeis) Hans Frauenfelder (Los Alamos) Robert Sauer (MIT) Elizabeth Getzoff (Scripps Research Harold Scheraga (Cornell) Institute) Klaus Schulten (Illinois) Philip Green (Univ. Washington) Rebecca Wade (EMBL, Heidelberg) Angela Gronenborn (NIH) Arieh Warshel (USC) Michael Levitt (Stanford) The meeting is planned to extend from the late afternoon of September 11 (registration and a light dinner/reception), through September 13, so that participants can depart early on September 14. The meeting will be held at the Academy's conference center in Irvine. If you would like to join us for this Colloquium, please send the attached registration form and your registration fee of $200 (which includes the cost of all meals for 11-13 September) as soon as possible to Dr. Edward Patte at the address indicated on the form. Please feel free to duplicate the form and extend the invitation to any students or colleagues you feel would contribute to this discussion. A block of rooms has been reserved at the hotel for the Colloquium. Please contact National Academies Travel (NAT) rather than calling the hotel directly, to make your reservations. Main reservations: 800-801-6696 or 202-298-9046 Receptionist: 202-298-1637 Fax: 202-338-2366 When contacting NAT, please refer to event name - Computational Biomolecular Science event code - BE02066 event date - September 11-13, 1997 hotel name - Hyatt Newporter Resort 1107 Jamboree Rd. Newport Beach, CA 92660 Please reserve your room before August 15, because the rooms will be released shortly after this date. We hope that you will be able to join us for this unusual Colloquium. Russell Doolittle (rdoolittle@ucsd.edu) J. Andrew McCammon (jmccammon@ucsd.edu) Peter G. Wolynes (wolynes@aries.scs.uiuc.edu) --------------------------------- cut here --------------------------------------- NATIONAL ACADEMY OF SCIENCES COLLOQUIUM "COMPUTATIONAL BIOMOLECULAR SCIENCE" REGISTRATION FORM Please complete and return this form to: Dr. Edward Patte NAS-146 National Academy of Sciences 2101 Constitution Avenue, NW Washington, DC 20418 FAX CREDIT CARD PAYMENTS ONLY: (202) 334-2153 Name________________________________________________________ Title_______________________________________________________ Company Name________________________________________________ Address_____________________________________________________ ____________________________________________________________ ____________________________________________________________ Phone_______________________________________________________ Email_______________________________________________________ Arrival Date___________________ Time________________________ Departure Date_________________ Time________________________ Registration fee of $200 (nonrefundable) includes all meals during meeting: ____ Registration check in U.S. dollars payable to "National Academy of Sciences" ___ Credit Card registration payable to "National Academy of Sciences" Charge to: ___Visa ___MasterCard ___American Express Card number_____________________________________ Expires_________ Signature_______________________________________ Date____________ My special dietary needs are as follows:_______________________________ _______________________________________________________________________ _______________________________________________________________________ From owner-genome-program@net.bio.net Thu Jul 17 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "James M. Ward" Newsgroups: bionet.molbio.genome-program Subject: human protein homologous to yeast Fun12 Date: 18 Jul 1997 09:02:42 -0700 Organization: UNC Chapel Hill Chemistry Department Lines: 14 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5qo432$9ak@net.bio.net> Reply-To: James_Ward@unc.edu NNTP-Posting-Host: net.bio.net Yeast Fun12 protein is highly homologous to proteins with unknown functions in Methanococcus jannaschii, Sulfolobus acidocaldarius and human. The middle part of the protein is also very similar to human mitochondria translation initiation factor 2, but other parts are not. Analysis of Fun12 sequence for mito. import signal showed it has a good possiblity to be targetted to mitochondria. I am wondering whether anybody have more information on Fun12 other than what is published in paper. Any suggestion about this group of protein? Yuelin Zhang Department of Chemistry University of North Carolina at Chapel Hill From owner-genome-program@net.bio.net Thu Jul 17 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Michal Opas Newsgroups: bionet.molbio.genome-program Subject: Calreticulin Meeting: 1st circular Date: 18 Jul 1997 09:02:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 323 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5qo43a$9bd@net.bio.net> NNTP-Posting-Host: net.bio.net We are delighted to announce that Calreticulin Workshop,=20 devoted to the structure and function of calreticulin and=20 related proteins, will take place on March 31 - April 2,=20 1998 in Banff, Alberta, Canada. The Workshop will provide=20 unique opportunity to meet and interact with the scientists=20 interested in calreticulin research in spectacular=20 surroundings of Banff National Park in Canadian Rocky=20 Mountains. We are sure that the Banff Calreticulin Workshop=20 will be an important forum to share the latest findings and=20 to develop future interactions. Calreticulin has been=20 implicated to play a role in almost every aspect of cell=20 biology as outlined in a brief overview below. We hope that=20 the Workshop will be useful to sort out some of the latest=20 discoveries and controversies concerning calreticulin and=20 implication of this protein in a variety of biological=20 systems. On the behalf of the Organizing Committee we would=20 like to invite you to participate in the Workshop.=20 The Calreticulin Workshop is a satellite meeting to the 8th=20 Fisher Winternational Symposium on Cellular and Molecular=20 Biology which will be held April 2-5, 1998, also at the=20 Banff Conference Centre. The Winternational Symposium,=20 which is co-sponsored by our Society and Fisher Scientific,=20 is held annually, with a different focus each year. The=20 theme for the 1998 meeting is : "Membrane Proteins in Health=20 and Disease." Further information about the Fisher=20 Winternational or the satellite meetings can be obtained by=20 visiting the Society's web site at=20 http://www.csbmcb.ca/english/bulletin/winternational.e.html=20 or by contacting the Chair of the Scientific Program=20 Committee by E-mail: Carol Cass . I hope you will participate in the Calreticulin Workshop. =20 If you would like to receive further information please send=20 a request (if possible, by e-mail) to Michal Opas at: m.opas@utoronto.ca =20 or at: Department of Anatomy & Cell Biology University of Toronto Medical Sciences Building Toronto, Ontario, M5S 1A8 Canada tel: (416) 978-8947 fax: (416) 978-3954 I look forward to hearing from you in the near future. For The Organizing Committee Sincerely yours Michal Opas Calreticulin, a multifunctional protein Calreticulin, 60 kDa Ca-binding protein [1], is a major=20 component of the endoplasmic reticulum (ER) of non-muscle=20 cells [2-7]. The protein is of high physiological=20 importance as it knockout is embryonic lethal [8]. Along=20 with a wide tissue distribution [9], calreticulin is present=20 in diverse animal and plant species [10]. calreticulin is a=20 resident ER protein as demonstrated by a variety of=20 biochemical and immunological techniques [1,3,4,6,11]. The=20 protein is synthesized with an N-terminal signal sequence=20 and it terminates with the KDEL sequence [3,12] which is=20 responsible for retrieval of proteins to the lumen of the ER=20 [13,14]. =20 Calreticulin functions in vivo as a Ca storage=20 protein [15,16]. It also has been well established that=20 calreticulin is a chaperone [17-21] and it shows similarity=20 in amino acid sequence to a part of calnexin, an ER membrane=20 chaperone [22]. The Ca storage and chaperone functions of=20 calreticulin are consistent with both the ER localization of=20 calreticulin and its structure. Stable overexpression of=20 calreticulin increases both cell-substratum and cell-cell=20 adhesiveness with concomitant upregulation of=20 adhesion-specific cytoskeletal protein, vinculin [23]. =20 Upregulation of calreticulin also affects adhesion-dependent=20 phenomena such as cell motility (which decreases) and cell=20 spreading (which increases). Downregulation of calreticulin=20 brings about inverse effects. In addition to the Ca=20 storage and chaperone function, calreticulin modulates gene=20 expression [24,25]. In vitro, calreticulin interaction with=20 the DNA binding domain of the glucocorticoid receptor=20 prevents the receptor from interacting with its=20 glucocorticoid response element [24]. Transcriptional=20 activation by glucocorticoid and androgen receptors in vivo=20 is inhibited in cells overexpressing full length=20 calreticulin [24,25]. Calreticulin itself is=20 stress-regulated by heat and heavy metals [26-28]. =20 Calreticulin has antithrombotic activity [29]. A host of=20 other putative calreticulin functions includes a role in=20 autoimmune diseases [30-34]. The protein affects=20 replication of the Rubella virus RNA [35,36]. In cytolytic=20 T lymphocytes it is found in the lytic granules where it may=20 play a role in killing of target cells [37]. In human=20 neutrophils calreticulin may contribute to the process of=20 phagocytosis [38]. In line with the reported functional=20 diversity, calreticulin was reported to be present in most=20 cellular compartments [10,11,37,39,40], including the outer=20 cell surface [41,42]. Recent hypotheses regarding=20 calreticulin function have been presented by Krause and=20 Michalak [43]. References 1. Ostwald TJ, MacLennan DH: Isolation of a high affinity=20 calcium binding protein from sarcoplasmic reticulum. J Biol=20 Chem 1974, 249:974-979. 2. Baksh S, Michalak M: Expression of calreticulin in=20 Escherichia coli and identification of its Ca2+ binding=20 domains. J Biol Chem 1991, 266:21458-21465. 3. Fliegel L, Burns K, Opas M, Michalak M: The=20 high-affinity calcium binding protein of sarcoplasmic=20 reticulum. Tissue distribution, and homology with=20 calregulin. Biochim Biophys Acta 1989, 982:1-8. 4. Opas M, Dziak E, Fliegel L, Michalak M: Regulation of=20 expression and intracellular distribution of calreticulin, a=20 major calcium binding protein of nonmuscle cells. J Cell=20 Physiol 1991, 149:160-171. 5. Milner RE, Baksh S, Shemanko C, Carpenter MR, Smillie L,=20 Vance JE, Opas M, Michalak M: Calreticulin, and not=20 calsequestrin, is the major calcium binding protein of=20 smooth muscle sarcoplasmic reticulum and liver endoplasmic=20 reticulum. J Biol Chem 1991, 266:7155-7165. 6. Michalak M, Baksh S, Opas M: Identification and=20 immunolocalization of calreticulin in pancreatic cells: no=20 evidence for "calciosomes". Exp Cell Res 1991, 197:91-99. 7. Michalak M, Milner RE, Burns K, Opas M: Calreticulin.=20 Biochem J 1992, 285:681-692. 8. Coppolino MG, Woodside MJ, Demaurex N, Grinstein S,=20 St-Arnaud R, Dedhar S: Calreticulin is essential for=20 integrin-mediated calcium signalling and cell adhesion.=20 Nature 1997, 386:843-847. 9. Tharin S, Dziak E, Michalak M, Opas M: Widespread tissue=20 distribution of rabbit calreticulin, a non-muscle functional=20 analogue of calsequestrin. Cell Tissue Res 1992, 269:29-37. 10. Opas M: The intracellular distribution and expression=20 of calreticulin. In Calreticulin, edited by Michalak M.=20 Georgetown: R.G. Landes; 1996:31-41. 11. Koch GLE: The endoplasmic reticulum and calcium=20 storage. BioEssays 1990, 12:527-531. 12. Fliegel L, Burns K, MacLennan DH, Reithmeier RAF,=20 Michalak M: Molecular cloning of the high affinity=20 calcium-binding protein (calreticulin) of skeletal muscle=20 sarcoplasmic reticulum. J Biol Chem 1989, 264:21522-21528. 13. Pelham HRB: Control of protein exit from the=20 endoplasmic reticulum. Annu Rev Cell Biol 1989, 5:1-23. 14. S=F6nnichsen B, F=FCllekrug J, Van PN, Diekmann W, Robinson=20 DG, Mieskes G: Retention and retrieval: Both mechanisms=20 cooperate to maintain calreticulin in the endoplasmic=20 reticulum. J Cell Sci 1994, 107:2705-2717. 15. Bastianutto C, Clementi E, Codazzi F, Podini P, De=20 Giorgi F, Rizzuto R, Meldolesi J, Pozzan T: Overexpression=20 of calreticulin increases the Ca2+ capacity of rapidly=20 exchanging Ca2+ stores and reveals aspects of their lumenal=20 microenvironment and function. J Cell Biol 1995,=20 130:847-855. 16. Liu N, Fine RE, Simons E, Johnson RJ: Decreasing=20 calreticulin expression lowers the Ca2+ response to=20 bradykinin and increases sensitivity to ionomycin in=20 NG-108-15 cells. J Biol Chem 1994, 269:28635-28639. 17. Nauseef WM, McCormick SJ, Clark RA: Calreticulin=20 functions as a molecular chaperone in the biosynthesis of=20 myeloperoxidase. J Biol Chem 1995, 270:4741-4747. 18. Wada I, Imai S, Kai M, Sakane F, Kanoh H: Chaperone=20 function of calreticulin when expressed in the endoplasmic=20 reticulum as the membrane-anchored and soluble forms. J Biol=20 Chem 1995, 270:20298-20304. 19. Nigam SK, Goldberg AL, Ho S, Rhode MF, Bush KT, Sherman=20 MY: A set of endoplasmic reticulum proteins possessing=20 properties of molecular chaperones includes Ca2+-binding=20 proteins and members of the thioredoxin superfamily. J Biol=20 Chem 1994, 269:1744-1749. 20. Otteken A, Moss B: Calreticulin interacts with newly=20 synthesized human immunodeficiency virus type 1 envelope=20 glycoprotein, suggesting a chaperone function similar to=20 that of calnexin. J Biol Chem 1996, 271:97-103. 21. Hebert DN, Foellmer B, Helenius A: Calnexin and=20 calreticulin promote folding, delay oligomerization and=20 suppress degradation of influenza hemagglutinin in=20 microsomes. EMBO J 1996, 15:2961-2968. 22. Bergeron JJM, Brenner MB, Thomas DY, Williams DB:=20 Calnexin: a membrane-bound chaperone of the endoplasmic=20 reticulum. Trends Biochem Sci 1994, 19:124-128. 23. Opas M, Szewczenko-Pawlikowski M, Jass GK, Mesaeli N,=20 Michalak M: Calreticulin modulates cell adhesiveness via=20 regulation of vinculin expression. J Cell Biol 1996,=20 135:1913-1923. 24. Burns K, Duggan B, Atkinson EA, Famulski KS, Nemer M,=20 Bleackley RC, Michalak M: Modulation of gene expression by=20 calreticulin binding to the glucocorticoid receptor. Nature=20 1994, 367:476-480. 25. Dedhar S, Rennie PS, Shago M, Leung-Hagesteijn C-Y,=20 Yang H, Filmus J, Hawley RG, Bruchovsky N, Cheng H, Matusik=20 RJ, Gigu=E8re V: Inhibition of nuclear hormone receptor=20 activity by calreticulin. Nature 1994, 367:480-483. 26. Nguyen TQ, Capra JD, Sontheimer RD: Calreticulin is=20 transcriptionally upregulated by heat shock, calcium and=20 heavy metals. Mol Immunol 1996, 33:379-386. 27. Dreher D, Vargas JR, Hochstrasser DF, Junod AF: Effects=20 of oxidative stress and Ca2+ agonists on molecular=20 chaperones in human umbilical vein endothelial cells.=20 Electrophoresis 1995, 16:1205-1214. 28. Conway EM, Liu L, Nowakowski B, Steiner-Mosonyi M,=20 Ribeiro SP, Michalak M: Heat shock-sensitive expression of=20 calreticulin. In vitro and in vivo up-regulation. J Biol=20 Chem 1995, 270:17011-17016. 29. Kuwabara K, Pinsky DJ, Schmidt AM, Benedict C, Brett J,=20 Ogawa S, Broekman MJ, Marcus AJ, Sciacca RR, Michalak M,=20 Wang F, Pan YC, Grunfeld S, Patton S, Malinski T, Stern DM,=20 Ryan J: Calreticulin, an antithrombotic agent which binds to=20 vitamin K-dependent coagulation factors, stimulates=20 endothelial nitric oxide production, and limits thrombosis=20 in canine coronary arteries. J Biol Chem 1995,=20 270:8179-8187. 30. Karska K, Tuckova L, Steiner L, Tlaskalova-Hogenova H,=20 Michalak M: Calreticulin--the potential autoantigen in=20 celiac disease. Biochem Biophys Res Commun 1995,=20 209:597-605. 31. Boehm J, Orth T, Van Nguyen P, S=F6ling H-D: Systemic=20 lupus erythematosus is associated with increased=20 auto-antibody titers against calreticulin and grp94, but=20 calreticulin is not the Ro/SS-A antigen. Eur J Clin Invest=20 1994, 24:248-257. 32. Zhu J, Newkirk MM: Viral induction of the human=20 autoantigen calreticulin. Clin Invest Med 1994, 17:196-205. 33. Ben-Chetrit E: The molecular basis of the SSA/Ro=20 antigens and the clinical significance of their=20 autoantibodies. Br J Rheumatol 1993, 32:396-402. 34. McCauliffe DP, Sontheimer RD: Molecular=20 characterization of the Ro/SS-A autoantigens. J Invest=20 Dermatol 1993, 100:73S-79S. 35. Atreya CD, Singh NK, Nakhasi HL: The rubella virus RNA=20 binding activity of human calreticulin is localized to the=20 N-terminal domain. J Virol 1995, 69:3848-3851. 36. Singh NK, Atreya CD, Nakhasi HL: Identification of=20 calreticulin as a rubella virus RNA binding protein. Proc=20 Natl Acad Sci USA 1994, 91:12770-12774. 37. Dupuis M, Schaerer E, Krause K-H, Tschopp J: The=20 calcium-binding protein calreticulin is a major constituent=20 of lytic granules in cytolytic T lymphocytes. J Exp Med=20 1993, 177:1-7. 38. Stendahl O, Krause K-H, Krischer J, Jerstrom P, Theler=20 JM, Clark RA, Carpentier JL, Lew DP: Redistribution of=20 intracellular Ca2+ stores during phagocytosis in human=20 neutrophils. Science 1994, 265:1439-1441. 39. Nakamura M, Moriya M, Baba T, Michikawa Y, Yamanobe T,=20 Arai K, Okinaga S, Kobayashi T: An endoplasmic reticulum=20 protein, calreticulin, is transported into the acrosome of=20 rat sperm. Exp Cell Res 1993, 205:101-110. 40. Dedhar S: Novel functions for calreticulin: =20 Interaction with integrins and modulation of gene=20 expression. Trends Biochem Sci 1994, 19:269-271. 41. White TK, Zhu Q, Tanzer ML: Cell surface calreticulin=20 is a putative mannoside lectin which triggers mouse melanoma=20 cell spreading. J Biol Chem 1995, 270:15926-15929. 42. Gray AJ, Park PW, Broekelmann TJ, Laurent GJ, Reeves=20 JT, Stenmark KR, Mecham RP: The mitogenic effects of the B =20 chain of fibrinogen are mediated through cell surface=20 calreticulin. J Biol Chem 1995, 270:26602-26606. 43. Krause K-H, Michalak M: Calreticulin. Cell 1997,=20 88:439-443. =20 =20 =20 =20 Dr. Michal Opas Department of Anatomy & Cell Biology University of Toronto 1 King's College Circle Medical Sciences Building Toronto, Ontario, M5S 1A8 Canada =20 phone: (416) 978-8947 fax: (416) 978-3954 e-mail: m.opas@utoronto.ca www homepage: http://www.utoronto.ca/anatomy/opas/start.htm=20 =20 From owner-genome-program@net.bio.net Sun Jul 20 23:00:00 1997 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.genome-program Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 21 Jul 1997 08:16:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 234 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5qvuh7$csu@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. From owner-genome-program@net.bio.net Mon Jul 21 23:00:00 1997 Path: biosci!biosci!not-for-mail From: ahp2343@bioch.tamu.edu (Andrew H Paterson) Newsgroups: bionet.molbio.genome-program Subject: Two postdoctoral positions in genome analysis Date: 22 Jul 1997 12:39:24 -0700 Organization: TAMU Lines: 38 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5r329c$sm0@net.bio.net> NNTP-Posting-Host: net.bio.net TWO POSTDOCTORAL POSITIONS: GENOME ANALYSIS Postdoctoral position, Unified molecular mapping of higher plant genomes. A postdoctoral position is available (1 Sept) to develop and apply new molecular methods for the comparative molecular analysis of diverse plant taxa based on expressed genes, building upon extensive databases of prior information (cf. GENETICS 138:499, 138:829, 141:391; PNAS-USA 92:6127; SCIENCE, 269:1714-1718; NATURE GENETICS 14:380-382) and existing YAC/BAC libraries. The successful candidate will have a Ph.D. and strong publication record in genetics, molecular biology, microbiology, or allied field, proven skills in mRNA/cDNA manipulation, a high level of professional motivation, excellent written and spoken English, and strong interpersonal skills. Applicants with experience in =B3cDNA selection=B2: methods using large DNA elements will be strongly preferred. Salary commensurate with experience, competitive benefits. To apply, mail full CV, reprints of 2-3 first-authored publications, addresses and phones of at least three professional references to Dr. Andrew Paterson, Plant Genome Mapping Laboratory, Texas A&M University, College Station, TX 77843. EMAIL ahp2343@bioch.tamu.edu. Affirmative Action/EOE. Postdoctoral position, Positional gene cloning in higher plants. A postdoctoral position is available (1 Sept, possibly earlier) to isolate well-mapped genes and QTLs that have played key roles in domestication of grasses, especially the Sh-1 gene of sorghum, using extensive databases of prior information (cf. GENETICS 138:499, 138:829, 141:391; PNAS-USA 92:6127; SCIENCE, 269:1714-1718; NATURE GENETICS 14:380-382), and existing YAC/BAC libraries. The successful candidate will have a Ph.D. and strong publication record in genetics, molecular biology, microbiology, or allied field, proven skills in cloning and analysis of large genomic DNAs, a high level of professional motivation, strong communication in English, and strong interpersonal skills. Salary commensurate with experience, competitive benefits. To apply, mail full CV, reprints of 2-3 first-authored publications, addresses and phones of at least three professional references to Dr. Andrew Paterson, Plant Genome Mapping Laboratory, Texas A&M University, College Station, TX 77843. EMAIL ahp2343@bioch.tamu.edu. Affirmative Action/EOE. From owner-genome-program@net.bio.net Mon Jul 21 23:00:00 1997 Path: biosci!biosci!not-for-mail From: NEWSMGR@selu.edu Newsgroups: bionet.molbio.genome-program Subject: Looking for homology search software for PC Date: 22 Jul 1997 12:39:26 -0700 Organization: Southeastern Louisiana University Lines: 26 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5r329e$smb@net.bio.net> NNTP-Posting-Host: net.bio.net Relay-Version: ANU News - V6.1B9 05/16/94 VAX/VMS V6.2-1H3; site alpha.selu.edu Path: alpha.selu.edu!news.lsu.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!g atech!smash.gatech.edu!news Newsgroups: bionet.molbio.genome-program Subject: Looking for homology search software for PC Message-ID: <33D21EA8.DE@ipst.edu> From: Nanfei Xu Date: Sun, 20 Jul 1997 10:20:24 -0400 Reply-To: nanfei.xu@ipst.edu Organization: IPST NNTP-Posting-Host: cas550-1.ipst.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Lines: 5 Is there any software available fpr PC that does the same thing as BLASTN, but using local database (sequences files on PC hard drive)? Thanks. Nanfei From owner-genome-program@net.bio.net Tue Jul 29 23:00:00 1997 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov Newsgroups: bionet.molbio.genome-program Subject: UNESCO on Human Genome and Human Rights Date: 30 Jul 1997 11:15:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5ro0cn$k0u@net.bio.net> NNTP-Posting-Host: net.bio.net **** Declaration On Human Genome And Human Rights (from EurekAlert) Paris, July 28 - A Draft Universal Declaration on the Human Genome and Human Rights with guidelines on genetic research and practices was adopted by an inter-governmental committee on Saturday at the end of a four-day meeting at UNESCO's Headquarters here. See http://www.eurekalert.org/releases/UNESCO_declare.html for the press release. More information on the Declaration and on the International Bioethics Committee can be found on UNESCO's web site at http://www.unesco.org/ibc. Further information can also be obtained from UNESCO's press service: tel: (33) 01 45 68 16 70, fax: (33) 01 45 68 56 52 From owner-genome-program@net.bio.net Thu Jul 31 23:00:00 1997 Path: biosci!biosci!not-for-mail From: william@amber.biology.gatech.edu (William S. Hayes) Newsgroups: bionet.molbio.genome-program Subject: Gene Discovery in Silico, Atlanta 1997 Date: 1 Aug 1997 06:43:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 164 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5rsp5v$sk@net.bio.net> NNTP-Posting-Host: net.bio.net GEORGIA TECH INTERNATIONAL CONFERENCE IN BIOINFORMATICS GENE DISCOVERY IN SILICO NOVEMBER 7 - 9, 1997 ATLANTA The focus of the conference is on gene identification and prediction of protein function using computer methods. SPONSORS: Georgia Tech SmithKline Beecham Gene Pro, Inc. DATES: Deadline for poster abstracts submission: October 3, 1997 Early registration ends: October 9, 1997 Conference schedule: Registration opens at 6:00pm on Thursday, November 6, (with the reception at 8:00pm). The program starts 8:00am Friday, November 7 and ends at noon Sunday, November 9. LOCATION: The conference will be held at Renaissance Atlanta Hotel Downtown located near the center of 1996 Olympic development, close to Fox Theatre & Georgia Tech AGENDA: The conference agenda includes 20 plenary talks (45 minutes for each talk and discussion) as well as poster sessions. PLENARY SPEAKERS: Stephen Altschul NCBI/NIH, Bethesda, MD Geoff Barton University of Oxford, Oxford, UK Peer Bork EMBL, Heidelberg & MDC, Berlin, Germany Mark Borodovsky Georgia Institute of Technology, Atlanta, GA Soren Brunak Technical University of Denmark, Copenhagen, Denmark Philipp Bucher ISREC, Lausanne, Switzerland Jean-Michel Claverie Structural & Genetic Information, CNRS, Marseille, France Jim Fickett SmithKline Beecham, King of Prussia, PA Terry Gaasterland Argonne National Lab & University of Chicago, Chicago, IL Michael Gribskov San Diego Supercomputer Center, San Diego, CA Roderic Guigo Insitute Municipal d'Investigcio Medica, Barcelona, Spain Steven Henikoff Fred Hutchinson Cancer Research Center, Seattle, WA Sam Karlin Stanford University, Stanford, CA Anthony Kerlavage The Institute for Genomic Research, Rockville, MD Eugene Koonin NCBI/NIH, Bethesda, MD Pavel Pevzner University of Southern California, Los-Angeles, CA Steven Salzberg Johns Hopkins University, Baltimore, MD Victor Solovyev Amgen, Inc., Thousand Oaks, CA Gary Stormo University of Colorado, Boulder, CO Michael Zhang Cold Spring Harbor Lab, Long Island, NY STEERING & PROGRAM COMMITTEE: Mark Borodovsky, Co-Chair, Georgia Tech Soren Brunak Technical University of Denmark Jim Fickett SmithKline Beecham Eugene Koonin, Co-Chair, NCBI/NIH GEORGIA TECH ORGANIZING COMMITTEE: Chair Prof. Mark Borodovsky, Schools of Biology & Mathematics Advisory board Prof. Leonid Bunimovich, School of Mathematics Prof. Shamkat Navathe, College of Computing Poster session Dr. Alex Lukashin, School of Biology Publicity William Hayes, School of Biology william@intron.biology.gatech.edu Registration and general events Laura Olson, Department of Continuing Education laura.olson@conted.gatech.edu POSTER SUBMISSION To apply for participation in a poster session, please send the title and one page abstract of your poster, by October 3, to Dr. Alex Lukashin, by e-mail: lukashin@amber.biology.gatech.edu (preferred method) or by FAX: (404) 894-0519. You may send the abstract earlier. The acceptance of the high quality poster will be confirmed within five days upon submission. REGISTRATION Registration Fee: Early (until October 9): $295, Academic/government - $245 Late: $345, Academic/government - $295 The registration fee includes handout materials and meals provided by Renaissance hotel chefs for the whole conference time. Hotel Reservations: This conference will be held at the Renaissance Atlanta Hotel Downtown. Call Renaissance Atlanta Hotel 404-881-6000 for reservation with Georgia Tech room rate of $99/night by October 9, 1997. Please mention the Bioinformatics/Georgia Tech conference. Travel Discounts: Delta Air Lines offers special fares to attendees of Georgia Tech programs. Certain restrictions may apply. For information and reservations, call 1-800-241-6760 and refer to file U0175 (for domestic flights only). To obtain more information & registration form, visit the WWW page: http://intron.biology.gatech.edu/~william/conference.html or contact us by e-mail: register@conted.gatech.edu Phone: (404) 894-2400 Fax: (404) 894-8925 From owner-genome-program@net.bio.net Thu Jul 31 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Sheryl Martin Newsgroups: bionet.molbio.genome-program Subject: New URL for Human Genome Project Information Research site Date: 1 Aug 1997 14:57:21 -0700 Organization: Oak Ridge National Lab, Oak Ridge, TN Lines: 28 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5rtm41$ctp@net.bio.net> Reply-To: s22@ornl.gov NNTP-Posting-Host: net.bio.net The Human Genome Project Information web site has been remodeled into two interest areas - research (technical) and general. Scientists now have a web site dedicated to their interests at http://www.ornl.gov/hgmis/research.html which can also be accessed via the general web site at http://www.ornl.gov/hgmis/ . Links to information on funding, event calendars, and abstracts of DOE research are there along with other information. Please give us a visit and let us know how we can better serve your interests. The material of interest to the general public remains at the home page at http://www.ornl.gov/hgmis/ . Both sites are funded by the U.S. Department of Energy Human Genome Program. ----------------------------------------------------------------- Sheryl Martin Web Architect Phone 423-574-7582, Fax -9888 Human Genome Management e-mail martinsa@ornl.gov Information System http://www.ornl.gov/hgmis Oak Ridge National Laboratory and Virtual Library: Genetics 1060 Commerce Park, MS 6480 http://www.ornl.gov/hgmis/genetics.html Oak Ridge, TN 37830 Sponsor: U.S. Department of Energy Human Genome Program