BioToolKit now provides 750 annotated links to Web tools for the study of nucleic acid, genome, and protein structure.
Gene-Finding Programs at Sanger
Updated versions of gene-finding programs (including FGENES, FGENESH, and FGENES-m variant for mammalian sequences) are available for use through the Sanger Web site. Also, the Gapped BLASTP program from the National Center for Biotechnology Information allows users to check a gene’s protein structure in the INFOGENEP database of finished and unfinished human sequences and receive the clone’s name and sequence. See the Web site for more information.
New Sequin Version
The National Center for Biotechnology Information has released Version 2.80 of Sequin, the sequence-submission and editing tool, for all platforms. This version is expected to be particularly useful for genome centers that annotate large records.
Tandem Repeat Tool
Gary Benson (Mount Sinai School of Medicine) has developed a program to find tandem repeats in DNA sequence data without prior knowledge of pattern repeat, pattern size, or number of copies. The current version finds pattern repeats ranging from 1 to 500 bases.
Users submitting a sequence (up to 2 Mb) in FASTA format will receive a summary table of repeats, including their location, size, number of copies, and nucleotide content. Clicking on an entry shows alignment against a consensus pattern, allowing the user to see the repeat pattern and mutation location.
Sequence Viewer, a free public software tool for viewing and analyzing DNA sequences, is available on the National Center for Genome Resources (NCGR) Web site. The NCGR tool was developed to fill the need for graphical representations of nucleotide sequences in the Genome Sequence DataBase and for detailed descriptions of sequence annotation. Sequence Viewer allows users to quickly find a sequence region that integrates with a gene rather than searching through a lengthy, complex flat-file report. It also can be used as a quality-control tool for readily locating mistakes in feature position.