Progress, and Applications
of the Human Genome Project
Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, May-June 1995; 7(1)
The Berkeley Drosophila Genome Project (BDGP) and FlyBase have announced Release 1.0 of the Macintosh CD-ROM version of the Encyclopaedia of Drosophila (EofD). This is the same version of the EofD DC-ROM that was distributed to registrants at the April 1995 Drosophila Research Conference in Atlanta. A new release is expected in September.
Release 1.0 of the EofD Macintosh CD-ROM version is a graphical interface based on ACeDB software developed for the Caenorhabditis elegans database, now a powerful browsing and querying tool for many genome databases. Release 1.0 contains much FlyBase data and all Berkeley Drosophila Genome Project data except DNA sequences. The long-term goal is to provide different views of the same comprehensive data set on both EofD and the FlyBase Home Page (http://morgan.harvard.edu).
EofD runs in native mode on higher-end Macintosh computers equipped with 68040 or PowerPC processors and a CD-ROM drive. It requires System 7.1 or higher (System 7.5 to use Guide help facilities), a minimum of 16 MB of RAM, and virtual memory of at least 32 MB. Minimal cost. [Orders: EofD; c/o Dawn Palmer; Biological Laboratories; Harvard University; 16 Divinity Ave.; Cambridge, MA 02138 (617/495-2906, Fax: -9300, firstname.lastname@example.org). EofD structure questions: email@example.com
Several new WWW database-search services developed by Randall Smith's group [Baylor College of Medicine (BCM)] are available through the BCM Search Launcher (http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html). The Search Launcher organizes searches related to molecular biology by function and provides a single point of entry for related searches. New tools and services include the following.
The University of Houston (UH) Gene-Server, managed by Dan Davison and funded by the National Science Foundation, the National Library of Medicine, and DOE, offers a number of Internet services for the genomics and molecular biology communities. These services include electronic access to software and data via ftp, Gopher, WWW, e-mail, and WAIS [see addresses below]. The Protein Information Resource (PIR), in release format and formatted for use in the GCG sequence analysis system, is available via ftp.
Another service from Gene-Server is Gene-Finder, to which a
series of servers for human gene identification and protein
secondary structure analysis were added recently in collaboration
with Victor Solovyev (BCM). These servers are fexh (find
exons in human genes), fgeneh (human gene modeling), hexon
(find internal exons), hspl (splice-site prediction for
human genes), nnssp (nearest-neighbor-based protein
secondary structure prediction), rnaspl (RNA splice-site
prediction), cdsb (bacterial coding-region prediction) and
ssp (segment-oriented protein secondary structure
prediction). Full details on each service can be obtained at firstname.lastname@example.org
Another server allows recognition of human and bacterial sequences (HBR) to test a library for Escherichia coli contamination by sequencing sample clones. The program calculates the probability of each sequence being human (P) or E.coli (1-P) and the total percentage of human and bacterial sequences in the set. The method is based on linear discriminant functions [Solovyev et al., Nucleic Acids Res. 22(24), 5156-63 (1994)].
These servers have been added to the Bioinformatics Information Engine at the Weizmann Institute of Science in Rehovot, Israel. In the future, Gene-Server will focus on providing multiple sequence alignment via WWW, e-mail, and client-server programs. Some multiple sequence alignment is now available from the BCM Sequence Launcher in collaboration with Randall Smith's group.
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