IMPROVEMENTS AND EXTENSIONS TO THE BLAST ALGORITHMS

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The BLAST family of protein and DNA database search programs constitute one of the key services offered by the NCBI. These programs are currently run on NCBI servers about 70,000 times during a typical weekday. This project represents an ongoing effort to improve and extend the functionality of these rogrmas. Progress this year has included: a) The development of an improved PSI-BLAST web page. This page allows the user to select or deselect specific alignments for inclusion in the construction of the PSI-BLAST position-specific score matrix used for the next database search. This facility allows for greatly refined searches, and an attendant increase in search sensitivity. The new web page also permits the user to select among a variety of amino acid substitution matrices tailored to varyng degrees of evolutionary divergence. This feature has been added as well to the standard BLAST page. b) The development of a new program, PHI-BLAST, for searching protein sequence databases using patterns as seeds. Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the Pattern-Hit Initiated BLAST (PHI-BLAST) program takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence.