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I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences.

However, many of the PSSM files contain lines of -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I rather than numerical values. What does it mean?

>     Last position-specific scoring matrix computed
>                 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
>         1 G  -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I  
>         2 N     4  -1  -2  -2   0  -1  -1   0  -2  -1  -1  -1  -1  -2  -1   1   0  -3  -2   0 
>         3 K    -2  -1   4   4  -3   0   1  -1   0  -3  -4   0  -3  -3  -2   0  -1  -4  -3  -3 
>         4 E     0  -3  -3  -3   9  -3  -4  -3  -3  -1  -1  -3  -1  -2  -3  -1  -1  -2  -2  -1 
>         5 K    -2  -2   1   6  -3   0   2  -1  -1  -3  -4  -1  -3  -3  -1   0  -1  -4  -3  -3 
>         6 A    -1   0   0   2  -4   2   5  -2   0  -3  -3   1  -2  -3  -1   0  -1  -3  -2  -2 
>         7 D    -2  -3  -3  -3  -2  -3  -3  -3  -1   0   0  -3   0   6  -4  -2  -2   1   3  -1 
>         8 R     0  -2   0  -1  -3  -2  -2   6  -2  -4  -4  -2  -3  -3  -2   0  -2  -2  -3  -3 
>         9 Q    -2   0   1  -1  -3   0   0  -2   8  -3  -3  -1  -2  -1  -2  -1  -2  -2   2  -3 
>        10 K    -1  -3  -3  -3  -1  -3  -3  -4  -3   4   2  -3   1   0  -3  -2  -1  -3  -1   3 
>        11 V    -1   2   0  -1  -3   1   1  -2  -1  -3  -2   5  -1  -3  -1   0  -1  -3  -2  -2 
>        12 V    -1  -2  -3  -4  -1  -2  -3  -4  -3   2   4  -2   2   0  -3  -2  -1  -2  -1   1 
>        13 S    -1  -1  -2  -3  -1   0  -2  -3  -2   1   2  -1   5   0  -2  -1  -1  -1  -1   1 
>        14 D    -2   0   6   1  -3   0   0   0   1  -3  -3   0  -2  -3  -2   1   0  -4  -2  -3 
>        15 L    -1  -2  -2  -1  -3  -1  -1  -2  -2  -3  -3  -1  -2  -4   7  -1  -1  -4  -3  -2 
>        16 V    -1   1   0   0  -3   5   2  -2   0  -3  -2   1   0  -3  -1   0  -1  -2  -1  -2 
>        17 A    -1   5   0  -2  -3   1   0  -2   0  -3  -2   2  -1  -3  -2  -1  -1  -3  -2  -3 
>        18 L     1  -1   1   0  -1   0   0   0  -1  -2  -2   0  -1  -2  -1   4   1  -3  -2  -2 
>        19 E     0  -1   0  -1  -1  -1  -1  -2  -2  -1  -1  -1  -1  -2  -1   1   5  -2  -2   0 
>        20 G     0  -3  -3  -3  -1  -2  -2  -3  -3   3   1  -2   1  -1  -2  -2   0  -3  -1   4 
>        21 A    -3  -3  -4  -4  -2  -2  -3  -2  -2  -3  -2  -3  -1   1  -4  -3  -2  11   2  -3 
>        22 L    -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1 
>        23 D    -2  -2  -2  -3  -2  -1  -2  -3   2  -1  -1  -2  -1   3  -3  -2  -2   2   7  -1 
>        24 M    -1   0   0   1  -3   4   4  -2   0  -3  -3   1  -1  -3  -1   0  -1  -2  -2  -2 
>        25 Y     0  -3  -3  -3   9  -3  -4  -3  -3  -1  -1  -3  -1  -2  -3  -1  -1  -2  -2  -1 
>        26 K    -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4 
>        27 L    -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1 
>        28 D    -1  -2  -3  -3  -1  -2  -3  -4  -3   3   3  -3   2   0  -3  -2  -1  -2  -1   2 
>        29 N  -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I  
>        30 S    -2   1  -1  -1  -2  -1  -2  -2  -1  -1  -1  -1  -2   0  -1   0   0  -1  -1  -3 
>        31 R     4   0  -2   1   4  -1  -3   0  -3   0  -3  -4   4  -1   0  -1  -3  -1   0  -4 
>        32 Y    -3  -1  -3  -4  -3  -3  -2  -3  -1  -3  -1  -1  -3  -3  -3  -1  -1  -1  -3  -2
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  • 2
    $\begingroup$ I don't know but guess that either something has gone wrong or those somehow represent insertions/deletions (gaps) $\endgroup$
    – Chris_Rands
    Jun 11, 2018 at 9:31
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    $\begingroup$ can you try running with more iterations? Running with a single one makes little sense I think $\endgroup$
    – Chris_Rands
    Jun 11, 2018 at 9:31
  • $\begingroup$ @Chris_Rands Perhaps more iterations would help, however, remote blast only allows one iteration, unless requerying. I could try running locally to see. Strangely, for SWISSPROT database (tiny compared to NR) it doesn't appear to happen (the instances of -I). $\endgroup$
    – Aalawlx
    Jun 12, 2018 at 17:44

1 Answer 1

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$\begingroup$

It means -inf. It has to do with how the PSSM score is calculated.

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  • $\begingroup$ That sounds very plausible, do you have a source/reference? Aren't pseudocounts normally added by default? will running >1 iteration change this? $\endgroup$
    – Chris_Rands
    Jun 12, 2018 at 13:32
  • $\begingroup$ Yes it appears to be minus infinity according to that wikipedia article. Strange how it was so hard to find this information. Thanks! Now I just need to figure out what to do about it since I need to encode this data. $\endgroup$
    – Aalawlx
    Jun 12, 2018 at 17:45
  • $\begingroup$ @Chris_Rands, if you have blast installed type in psiblast -help. You'll see that pseudocount is set by default to 0. $\endgroup$
    – benn
    Jun 12, 2018 at 19:44
  • $\begingroup$ On NCBI PSI-BLAST web interface it says "Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented." $\endgroup$
    – Chris_Rands
    Jun 12, 2018 at 20:27
  • $\begingroup$ @Chris_Rands, did you read psiblast -help or not? That is something else than a web interface. $\endgroup$
    – benn
    Jun 13, 2018 at 7:15

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