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Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News, November 1993: 5(4)
In keeping with the DOE policy of providing timely access to genome data, the Human Genome Center at Lawrence Berkeley Laboratory (LBL) is making data available to other members of the research community from its Chromosome 21 Physical Mapping Database (21Bdb). 21Bdb was developed by the genome center and its Genome Computing Group.
This initial release (1.1) of 21Bdb covers several different types of data and their relationships, including 250 sequence tagged site (STS) markers, 102 P1 clones, 816 yeast artificial chromosome (YAC) clones, 217 cDNA clones, and 160 DNA sequences. New LBL data and revisions will be added weekly. Users are encouraged to add questions and comments.
21Bdb extends ACEDB, which was originally developed for Caenorhabditis elegans and allows all parts of the database to be cross-referenced, resulting in a rich web of interconnections. The ACEDB user interface permits exploration of data via 'point and click' with the workstation mouse or with a versatile query facility developed by LBL. LBL staff are collaborating with the original ACEDB authors, Richard Durbin (Medical Research Council, U.K.) and Jean Thierry-Mieg (CNRS, France), to continue its development. 21Bdb is one of several databases that LBL is helping to develop for different genomes, including those of Drosophila melanogaster, soybean, wheat, and forest trees.
The 21Bdb STS window displays columns of ordered physical map markers, including STSs from Genethon and LBL, YACs, P1s and cDNAs localized to the STSs, and radiation hybrid cell-line breakpoints. The map is displayed graphically with zoom capability, and users can ''click'' individual biological elements to bring up details on any object, such as STS primer sequence and product size and cDNA sequence. Authorized users can rearrange map markers by''drag and drop'' or by respecifying position. Other ACEDB modules allow users to display and search DNA sequences for open reading frames, genes, and other features and compare multiple maps that share common markers.
Remote access to the full Unix version of 21Bdb is available to anyone on the Internet running X-windows software, including Unix workstations and Macintosh and IBM-PC computers. Remote users run 21Bdb at LBL with the graphic interface display on their own local computers. Those familiar with Unix and ACEDB may copy the entire 21Bdb database and ACEDB software. For more detailed information, use anonymous ftp to access genome.lbl.gov and see the files in /pub/21Bdb, or send e-mail to 21Bdb@genome.lbl.gov.
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The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v5n4).
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.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.
