HUM-MOLGEN archive: COMP: New WWW-based DNA and protein sequence analysis tools

************************************************************************ HUM-MOLGEN COMPuters ************************************************************************ Dear HUM-MOLGENeticists, This COMPUTERS message contains 1 message. 1) Randall Smith New WWW-based DNA and protein sequence analysis tools This section introduces interesting Internet resources and is open for discussions in the field of Computational Genetics. Please mail your suggestions for Internet-Highlights to HUM-MOLGEN@nic.surfnet.nl (Subject: COMP: ...). Frank S. Zollmann (Editor HUM-MOLGEN) ************************************************************************ 1)From: Randall Smith <rsmith@DOT.IMGEN.BCM.TMC.EDU> Subj. : New WWW-based DNA and protein sequence analysis tools The Human Genome Center, Baylor College of Medicine, is pleased to announce two new WWW services which speed the analysis of DNA and protein sequences. These services are now available via the "BCM Search Launcher" Web page: http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html (The BCM Search Launcher organizes and simplifies molecular biology-related search and analysis services available on the WWW. It provides a single point-of-entry for related services, for example, a single page for launching sequence searches using standard parameters). 1) Multiple Sequence Alignment Server CLUSTAL-W (Thompson, Higgins, and Gibson, 1994), MAP (Huang, 1994), and PIMA (Smith and Smith, 1992) multiple sequence alignments can now be run remotely on our server via the Search Launcher. The server uses Don Gilbert's readseq program to input sequences in any one of a variety of formats (e.g., FASTA, GCG, NBRF, EMBL). Both DNA and protein multiple alignments can be performed. 2) BEAUTY searches of a new Annotated Protein Sequence Database The Annotated Sequences database consists of all Entrez protein sequences containing at least one domain or site (see below). BEAUTY performs a standard BLAST search of this database and generates a graphic for each database hit showing the locations of all annotated domains and sites with respect to the locations of the hits within each matched sequence. SRS links to the appropriate record in the Entrez, PROSITE, BLOCKS, and PRINTS databases are also provided. These enhancements make it much easier to detect functionally significant matches in BLAST database searches. A database of annotated domains/sites was created by 1) scanning the NCBI's Entrez database for protein sequence records containing annotations of domains and sites, and storing the location of all such regions, 2) matching each Entrez protein sequence against the sequence motifs in the PROSITE pattern database, and storing the location of each hit, 3) extracting the locations of the conserved blocks within the sequences represented in the BLOCKS database, and 4) extracting the locations of all domains identified in the sequences in the PRINTS protein fingerprint database. The Annotated Sequences database currently contains 55,566 sequences. A more detailed program description, is available at: http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html ------------------------------------------------------------------------ Kim Worley, Brent Wiese, and Randall Smith Human Genome Center, Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine, Houston, TX 77030 USA kworley@bcm.tmc.edu, brent@bcm.tmc.edu, rsmith@bcm.tmc.edu ------------------------------------------------------------------------ *********************** end of message *********************************