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Human Genome News, July-August 1995; 7(2):9

Informatics, Software, and Database Resources

Informatics Resources

EBI Releases RHdb
The European Bioinformatics Institute (EMBL outstation, Hinxton) has announced the release of RHdb, a new database for radiation hybrid mapping raw data. Flat files (ASCII text) are accessible at ftp://ftp.ebi.ac.uk/pub/databases/RHdb or http://www.ebi.ac.uk:80/RHdb in exp.dat (experimental conditions), panel.dat (panel information), and rh.dat (raw mapping data). Data submissions: see format at http://www.ebi.ac.uk/RHdb; database questions: datalib@ebi.ac.uk with rhdb on the subject line.

Haplotyping Programs Available
The haplotyping programs SIMCROSS and SIMWALK, developed by Daniel Weeks and colleagues (University of Oxford and University of Pittsburgh), are now available in the pub directory by anonymous ftp ftp://watson.hgen.pitt.edu/pub). These are programs to generate optimal haplotype configurations on general pedigrees by using a likelihood-based approach for correctly taking intermarker recombination fractions into account. [Contact: Daniel Weeks (Fax: 412/624-3020 or +44-1865/742-196, dweeks@watson.hgen.pitt.edu or daniel.weeks@well.ox.ac.uk)]

Software, Database Resources

Stanford University

CENSOR Software. Jerzy Jurka and Paul Klonowski (Stanford University) have added CENSOR software to the Pythia program developed by Aleksander Milosavljevic (Argonne National Laboratory) and Jurka. This addition should speed up and facilitate identification, analysis, annotation, and removal (censoring) of repetitive DNA from sequences. To run online CENSOR, send help message to pythia@anl.gov. The original software is available from the National Center for Biotechnology Information (NCBI).

Repbase. The Repbase database for screening human repetitive DNA sequences was published and released electronically in 1992 with DOE support. Reference collections by Jurka's group now contain 434 prototypic examples and consensus sequences for rodents, other mammals, nonmammalian vertebrates, invertebrates, and plants. Only the human reference collection is being updated regularly. In addition to complex repeats, the group has compiled the 67 most abundant simple repeats and, with NCBI support, 38 collections of known repeats present but not necessarily annotated in GenBank primate sequences. Repbase is accessed through the NCBI address above. Jurka (jurka@gnomic.stanford.edu) would like to receive user comments on CENSOR and Repbase.

Jackson Laboratory

The following two resources are supported by NCHGR through a grant to Janan Eppig. [Information: Mouse Genome Informatics User Support (207/288-6445, mgi- help@informatics.jax.org)].

Encyclopedia of the Mouse Genome. The Encyclopedia of the Mouse Genome --a software tool that provides a graphic display of mouse chromosome maps --runs on a Macintosh, Sun, or DEC Alpha workstation. Data files include the most current Chromosome Committee reports and Massachsetts Institute of Technology mouse genetic maps. The encyclopedia can also interact with the Mouse Genome Database (MGD).

Current versions of the software (1.0A13 for Macintosh, 3.0A2 for UNIX) and data files can be downloaded from WWW using the "Encyclopedia of the Mouse Genome" link on the Mouse Genome Infromatics Home Page (http://www.informatics.jax.org). Instructions are also provided to configure Netscape and Mosaic for MGD and encyclopedia interaction.

MGD. (http://www.informatics.jax.org) and a mirror site for the European research community (url no longer available) are now available on the WWW. Improvements in Release 2.0 include a PostScript map tool for making printouts of mouse genetic maps; an option to view composite data sets for recombinant inbred strains; and access to Michael Festing's (University of Leicester, U.K.) "Listing of Inbred Strains."

In addition, changes to MGD query forms include a banner at the top of each form providing "buttons" for easier navigation within MGD. The Mammalian Homology query form has been redesigned, and the fields "Modification Date" and "Accession number" have been added to several query forms. Bibliographic records now include abstracts, if available, and the Citations query form includes an "Abstract" field to search for citations containing specified text in the abstracts. Finally, the Mouse Genetic Marker Information query form enables users to specify a "Type" of marker to search by "Cytogenetic Band" location.

EUCIB Database on WWW

The European Collaborative Interspecific Backcross (EUCIB) provides resources for a high-resolution genetic map that will form the basis for constructing a complete physical map of the mouse genome. The MBx database, which supports the mapping effort by storing mouse, locus, and probe data, is now available on WWW at http://www.hgmp.mrc.ac.uk/GoneAway/MBx.html.

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Human Genome Program, U.S. Department of Energy, Human Genome News (v7n2).

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.