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Human Genome News, May-June 1995; 7(1)

Informatics Resources

Harvard Releases Encyclopaedia of Drosophila

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, eofd-sales@morgan.harvard.edu). EofD structure questions: eofd@fly2.berkeley.edu

Baylor WWW Tools Available for Database Searching, Multiple Alignment

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.

• BEAUTY (BLAST Enhanced Alignment Utility) incorporates information on the locations of conserved and annotated domains and sites (drawn from a local database and the Entrez, PIR, SWISS-PROT, PROSITE, BLOCKS, and PRINTS databases) directly into BLAST search results. These enhancements greatly facilitate detection of weak but functionally significant matches in BLAST database searches. (A more detailed description is available at http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html).

• Interface to the National Center for Biotechnology Information's BLAST server adds links to the Entrez and SRS (Sequence Retrieval System) databases to BLAST search results. These links provide easy access to related information such as Medline abstracts.

• Multiple Sequence Alignment Server: CLUSTAL-W, MAP, and Pattern-Induced Multiple Alignment (PIMA) alignments can be run remotely on the BCM server, which uses the readseq program to input sequences in one of several formats (e.g., FASTA, MSF, NBRF, EMBL). Both DNA and protein multiple alignments can be performed.

• FASTAPAT and BLASTPAT Pattern Database Search Tools: Modified versions of FASTA and BLAST rapidly and sensitively search the PIMA Pattern Database for matches to protein sequences not identified by standard searches. A more detailed description of these programs is available (http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/fastpat.html).

Gene-Server Offers Internet Services

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 service@bchs.uh.edu with man in the subject line (e.g., man hexon.)

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.

• Gene-Server questions (davison@uh.edu)
• Gopher (gopher.bchs.uh.edu or gopher://gopher.bchs.uh.edu): PIR sequence-retrieval pointers to other Bio-Gophers and some local information
• WWW (http://www.bchs.uh.edu): ftp site, software descriptions, and yellow pages of molecular biology software
• WAIS (www.bchs.uh.edu): indexed software descriptions
• Ftp (ftp.bchs.uh.edu): PIR releases and Macintosh, DOS, UNIX, and VMS molecular biology software
• E-mail (gene-server@bchs.uh.edu): molecular biology software and data

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