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 an option uploading an ASN.1 PSSM file you have saved.
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 two or more 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 (the link is currently at the top/center in the Download menu, you need the PssmWithParameters ASN.1. Currently, this file will only work if you have uploaded or pasted a FASTA sequence file in the box. It does not work if only an Accession number was provided.
Download the PssmWithParameter file, and upload using: