PSIBLAST
PSIBLAST = Position Specific Iterative BLAST refers to a feature of BLAST in which a profile (or position specific scoring matrix, PSSM) is constructed (automatically) from a multiple alignment of the highest scoring hits in an initial BLAST search. The PSSM is generated by calculating position-specific scores for each position in the alignment. Highly conserved positions receive high scores and weakly conserved positions receive scores near zero. The profile is used to perform a second (etc.) BLAST search and the results of each "iteration" used to refine the profile. This iterative searching strategy results in increased sensitivity.
Manual: http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html
INPUT = Protein Sequences
TEST FILES
Input sequence file: psiblast_in.txt
Input alignment file (-B option): psiblast-Balignmentfile.txt
Output file: psiblast_output.txt
