BLAST

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Chapter 13: NCBI-BLAST Reference

blastpgp Parameters (PSI-BLAST

and PHI-BLAST)

blastpgp is the program used to run PSI-BLAST and PHI-BLAST. These programs are

specialized protein BLAST comparisons that are more sensitive than the standard

BLASTP search. PSI-BLAST considers position-specific information when searching

for significant hits. PHI-BLAST uses a pattern, or profile, to seed an alignment,

which is then extended by the normal BLASTP algorithm.

PSI-BLAST

PSI-BLAST (position-specific iterated BLAST) uses a specialized scoring matrix that

assigns scores to each position (hence, position-specific) in the query sequence based

on alignments defined by consecutive iterations of searches (hence, iterated). The

specialized matrix is a position-specific scoring matrix (PSSM) that assigns a score for

every amino acid at each position in the query sequence (See Figure 13-1).

Figure 13-1 shows a portion of a PSSM calculated for the coelacanth Hoxa11 protein

(AAG39070). The query amino acids are numbered in the left column with the posi-

tion-specific scores for each of the 20 amino acids shown across each row. The

diverse scores of the three Tyrosines (Y) at positions 1, 7, and 8 highlight the posi-

tion-specific aspect of this scoring scheme compared to traditional BLAST matrices,

which ...