Entering edit mode
7.6 years ago
xlong2
•
0
Hi. I'm generating pssm for my protein sequence alignment using the command:
psiblast -db cluster_sequences_blastdb -in_msa alignment_file.fasta -out_ascii_pssm pssm_file_name
But the pssm generated does not seem to have pseudocount:
2 Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudo counts
3 A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
4 1 Q -1 0 0 -1 -3 4 1 -2 5 -3 -2 0 -1 -2 -2 0 -1 -2 0 -2 0 0 0 0 0 50 0 0 50 0 0 0 0 0 0 0 0 0 0 0 0.57 0.00
5 2 Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.66 0.00
6 3 Y -1 4 -1 -2 -3 0 -1 -3 1 -2 -1 1 -1 1 -2 -1 -1 1 4 -2 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0.50 0.00
7 4 N 0 -1 4 1 -2 0 0 0 0 -3 -3 0 -2 -3 -1 3 1 -3 -2 -2 0 0 50 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0.45 0.00
8 5 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0.46 0.00
9 6 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0.87 0.01
10 7 S 1 -1 0 -1 -1 0 0 -1 -1 -1 -2 0 -1 -2 -1 3 3 -2 -2 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 0 0 0.39 0.00
but based on http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647318/ psiblast seems to employ column data dependent method to generate pseudocount for each column. Could anyone point out what I may have missed? Thank you.