The FASTA SSEARCH and PRSS programs can use the Smith-Waterman algorithm to compare a BLAST Position Specific Scoring Matrix (Altschul, et al, 1997 [Entrez]) to a sequence database (SSEARCH) or evaluate the statistical significance of a PSSM:sequence alignment using PRSS. Searches and shuffles using SSEARCH or PRSS use both a query sequence and an encoded Position Specific Scoring Matrix (PSSM).
Checking the option: Use PSSM:
presents two options for either uploading an ASN.1 PSSM file you have saved, or downloading PSI-BLAST RID file.
PSSMs can be obtained either with (1) the CHAPS program, which takes a set of sequences, aligns them with Clustal (), and then produces a PSSM using PSI-BLAST, or (2) directly from the NCBI PSI-BLAST program after a search. PSSM files saved from CHAPS can be uploaded using the:
PSSM's are also available from NCBI's PSI-BLAST WWW site. After you have performed several iterations of a PSI-BLAST search, you can evaluate the statistical significance of the expectation value estimates from the last iteration by downloading the NCBI PSSM using the RID from the search, and copying it into: