Question: generating pssm and account for pseudocount
0
gravatar for xlong2
3.5 years ago by
xlong20
xlong20 wrote:

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.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by xlong20
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