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Searches with PSI-BLAST PSSM's

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:


Upload PSSM ASN.1 file


option that appears when SSEARCH or PRSS is selected as the comparison program. If you upload a PSSM ASN.1 file, you must be certain that you use the first sequence in the multiple alignment as the query sequence - the SSEARCH and PRSS programs detect differences between the query sequence and the sequences in the PSSM, and will report an error if they differ.

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:


Upload PSSM ASN.1 file


Once again, the query sequence used for the search or shuffle must match the first sequence used in the PSI-BLAST search.


Search Databases with FASTA | Statistical Significance from Shuffles | Get FASTA