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Human Genome News Archive Edition

Human Genome News, November 1993: 5(4)


Software, Services, Electronic Data Access

This material sent to HGMIS is not reviewed or evaluated and is not a comprehensive list.


ACEDB is a Windows-based Caenorhabditis elegans database containing genomic data that includes strain and sequence, physical and genetic maps, and a bibliography. Contact: Richard Durbin; Medical Research Council Laboratory of Molecular Biology; Cambridge CB2 2QH, England (+44/223-248011, Internet: rd@mac-lmb.cam.ac.uk).

GeneScape is a relational database of Escherichia coli genomic map data for Macintosh computers. It allows access to information being collected in datasets of DNA sequences (EcoSeq), maps (EcoMap), and genetic data (EcoGene). Available by anonymous ftp to ncbi.nlm.nih.gov.

Yeast Genome Database is under development. The Yeast Genome Information Server can be accessed by Gopher atgenome.stanford.edu.

FlyBase is a Drosophila melanogaster database being built and maintained by Michael Ashburner (University of Cambridge, England); Bill Gelbart (Harvard University); Thom Kaufman and Kathy Matthews (both at Indiana University); and John Merriam (University of California, Los Angeles). This database will continue the tradition of the RedBook but in an electronically accessible and searchable form. Preliminary and working parts of FlyBase are available at the Indiana University Bioarchive, which can be accessed by ftp from ftp.bio.indiana.edu or by Gopher at fly.bio.indiana.edu.

Screening Service for Chromosome 21 Yeast Artificial Chromosomes (YACs) is available, and a P1 library screening service is being started. Contact: David Patterson; Eleanor Roosevelt Institute for Cancer Research (303/333-4515, Fax: -8423, Internet: davepatt@druid.hsc. colorado.edu)

Chromosome 17 YAC Screening Service is available. Contact: Craig Chinault (713/798-6075, Internet: chinault@bcm.tmc.edu). For electronic access to information on chromosome 17 YACs, send e-mail to yaclab@bcm.tmc.edu.

Chromosome 9 Anonymous FTP Server has been established by John Attwood (University College, London;john@mrc-hbgu.ucl.ac.uk). The address diamond.gene. ucl.ac.uk (128.40.82.1) may be used to download chromosome 9 workshop abstracts, figures, and reports (to be published in Cytogenetics and Cell Genetics). After connecting to the server, users should log in as anonymous and give their electronic mail address as a password. The workshop files are in the directory /pub/c9workshop in both plain text and postscript format. An electronic mailing list has also been arranged for the chromosome 9 community. To be added to the list, send e-mail to Attwood at the above address.

GRAM V1.4 (Genomic Restriction Map Assembly), a software tool for assembling restriction maps from single-digest data, is being distributed by the Center for Human Genome Studies at Los Alamos National Laboratory (LANL). The principal author, designer, and developer of GRAM is Carol Soderlund, a 1991 DOE Human Genome Distinguished Postdoctoral Fellow.

Using single-digest restriction fragments as input, GRAM outputs one or more plausible restriction maps with clone alignment. The exact restriction map can rarely be generated due to the complexity of the problem and the uncertainty in the data. Therefore, the GRAM algorithm uses a set of heuristics and stochastic algorithms to approximate the solution. With GRAM's interactive graphics, the user can query the GRAM solution and correct outstanding errors. Example execution times for the GRAM algorithms are 3 seconds on an input of 14 clones with a restriction map of 24 fragments and 18 seconds on 47 clones with a restriction map of 72 fragments. GRAM is available from LANL without charge, and the following can be obtained through anonymous ftp: the GRAM source code, which is written in C and uses Athena widgets; a postscript file of the GRAM manual; a set of sample input files; and the executable software that was compiled on a Sun Sparcstation and statically linked with the X11R4 libraries. For more information on GRAM, contact Soderlund [LANL; T-10 MS K710; Los Alamos, NM 87545 (Internet: cari@t10.lanl.gov)].

GDB-Lite Tool Developed for Macintosh. GDB-Lite is a user-friendly browsing and data-entry tool developed for the Macintosh by Randall Smith and Joanna Power of Baylor College of Medicine. With the point-and-click interface of the 4th Dimension (4D) relational database management system, investigators can use the automatic join features to incorporate data from several Genome Data Base (GDB) tables. They can also enter their own probe and locus information directly into a compatible format for electronic submisssion to GDB. User documentation and the 4D structure and data files for GDB-Lite may be obtained by Internet anonymous ftp from gc.bcm.tmc.edu (subdirectoryGDB-Lite_0.3). GDB-Lite requires a Macintosh with a hard disk, monochrome or high-resolution monitor of at least 12 in., and the 4D Runtime Version 3.0 from the software manufacturer ACIUS (Cupertino, CA). For more information, e-mail to gdb-lite@bcm.tmc.edu or contact Power (713/798-4689, Fax: -5386).

PROSEARCH: Fast Searching of Protein Sequences. ProSearch is a computer program that allows rapid identification of biologically relevant motifs in protein sequences and generation of a report describing the patterns and their locations. Although user-developed patterns can be added to any search, ProSearch currently uses the 690 different patterns in the PROSITE database of Amos Bairoch (University of Geneva), which consists of protein motifs characteristic of biochemical functions or protein families in the SWISS-PROT database. ProSearch, written in the AWK computer language that can run on all platforms commonly found in laboratories, is available by anonymous ftp from receptor.mgh.harvard.edu. The program was developed by Lee F. Kolakowski, Jr. [Massachusetts General Hospital and Harvard Medical School (MGH HMS)]; Jack Leunissen (University of Nijmegen, Netherlands); and Joseph Smith (University of Pennsylvania) [BioTechniques 13 (6), 919-21 (1992)]. Contact: Lee Kolakowski; MGH HMS; 149 13th St.; Charlestown, MA 02129 (Fax: 617/726-5669; Internet:kolakowski@helix.mgh.harvard.edu).


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Human Genome Program, U.S. Department of Energy, Human Genome News (v5n4).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.