Answers.Body: <p>It means -inf. It has to do with how the <a href="https://en.wikipedia.org/wiki/Position_weight_matrix" rel="nofollow noreferrer">PSSM</a> score is calculated.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T13:32:10.317Z
Answers.Text: That sounds very plausible, do you have a source/reference? Aren't pseudocounts normally added by default? will running >1 iteration change this?
Answers.UserDisplayName: Chris_Rands
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T17:45:55.903Z
Answers.Text: 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.
Answers.UserDisplayName: Aalawlx
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T19:44:33.563Z
Answers.Text: @Chris_Rands, if you have blast installed type in `psiblast -help`. You'll see that pseudocount is set by default to `0`.
Answers.UserDisplayName: benn
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T20:27:41.297Z
Answers.Text: 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."
Answers.UserDisplayName: Chris_Rands
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-13T07:15:39.653Z
Answers.Text: @Chris_Rands, did you read `psiblast -help` or not? That is something else than a web interface.
Answers.UserDisplayName: benn
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T13:14:37.460Z
Answers.LastActivityDate: 2018-06-12T13:14:37.460Z
Answers.UserDisplayName: benn
Body: <p>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.</p>
  
  <p>However, many of the PSSM files contain lines of <code>-I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I</code> rather than numerical values.  What does it mean?</p>
  
  <pre><code>&gt;     Last position-specific scoring matrix computed
  &gt;                 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
  &gt;         1 G  -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I  
  &gt;         2 N     4  -1  -2  -2   0  -1  -1   0  -2  -1  -1  -1  -1  -2  -1   1   0  -3  -2   0 
  &gt;         3 K    -2  -1   4   4  -3   0   1  -1   0  -3  -4   0  -3  -3  -2   0  -1  -4  -3  -3 
  &gt;         4 E     0  -3  -3  -3   9  -3  -4  -3  -3  -1  -1  -3  -1  -2  -3  -1  -1  -2  -2  -1 
  &gt;         5 K    -2  -2   1   6  -3   0   2  -1  -1  -3  -4  -1  -3  -3  -1   0  -1  -4  -3  -3 
  &gt;         6 A    -1   0   0   2  -4   2   5  -2   0  -3  -3   1  -2  -3  -1   0  -1  -3  -2  -2 
  &gt;         7 D    -2  -3  -3  -3  -2  -3  -3  -3  -1   0   0  -3   0   6  -4  -2  -2   1   3  -1 
  &gt;         8 R     0  -2   0  -1  -3  -2  -2   6  -2  -4  -4  -2  -3  -3  -2   0  -2  -2  -3  -3 
  &gt;         9 Q    -2   0   1  -1  -3   0   0  -2   8  -3  -3  -1  -2  -1  -2  -1  -2  -2   2  -3 
  &gt;        10 K    -1  -3  -3  -3  -1  -3  -3  -4  -3   4   2  -3   1   0  -3  -2  -1  -3  -1   3 
  &gt;        11 V    -1   2   0  -1  -3   1   1  -2  -1  -3  -2   5  -1  -3  -1   0  -1  -3  -2  -2 
  &gt;        12 V    -1  -2  -3  -4  -1  -2  -3  -4  -3   2   4  -2   2   0  -3  -2  -1  -2  -1   1 
  &gt;        13 S    -1  -1  -2  -3  -1   0  -2  -3  -2   1   2  -1   5   0  -2  -1  -1  -1  -1   1 
  &gt;        14 D    -2   0   6   1  -3   0   0   0   1  -3  -3   0  -2  -3  -2   1   0  -4  -2  -3 
  &gt;        15 L    -1  -2  -2  -1  -3  -1  -1  -2  -2  -3  -3  -1  -2  -4   7  -1  -1  -4  -3  -2 
  &gt;        16 V    -1   1   0   0  -3   5   2  -2   0  -3  -2   1   0  -3  -1   0  -1  -2  -1  -2 
  &gt;        17 A    -1   5   0  -2  -3   1   0  -2   0  -3  -2   2  -1  -3  -2  -1  -1  -3  -2  -3 
  &gt;        18 L     1  -1   1   0  -1   0   0   0  -1  -2  -2   0  -1  -2  -1   4   1  -3  -2  -2 
  &gt;        19 E     0  -1   0  -1  -1  -1  -1  -2  -2  -1  -1  -1  -1  -2  -1   1   5  -2  -2   0 
  &gt;        20 G     0  -3  -3  -3  -1  -2  -2  -3  -3   3   1  -2   1  -1  -2  -2   0  -3  -1   4 
  &gt;        21 A    -3  -3  -4  -4  -2  -2  -3  -2  -2  -3  -2  -3  -1   1  -4  -3  -2  11   2  -3 
  &gt;        22 L    -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1 
  &gt;        23 D    -2  -2  -2  -3  -2  -1  -2  -3   2  -1  -1  -2  -1   3  -3  -2  -2   2   7  -1 
  &gt;        24 M    -1   0   0   1  -3   4   4  -2   0  -3  -3   1  -1  -3  -1   0  -1  -2  -2  -2 
  &gt;        25 Y     0  -3  -3  -3   9  -3  -4  -3  -3  -1  -1  -3  -1  -2  -3  -1  -1  -2  -2  -1 
  &gt;        26 K    -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4  -4 
  &gt;        27 L    -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1 
  &gt;        28 D    -1  -2  -3  -3  -1  -2  -3  -4  -3   3   3  -3   2   0  -3  -2  -1  -2  -1   2 
  &gt;        29 N  -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I -I  
  &gt;        30 S    -2   1  -1  -1  -2  -1  -2  -2  -1  -1  -1  -1  -2   0  -1   0   0  -1  -1  -3 
  &gt;        31 R     4   0  -2   1   4  -1  -3   0  -3   0  -3  -4   4  -1   0  -1  -3  -1   0  -4 
  &gt;        32 Y    -3  -1  -3  -4  -3  -3  -2  -3  -1  -3  -1  -1  -3  -3  -3  -1  -1  -1  -3  -2
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-11T09:31:21.090Z
Comments.Text: I don't know but guess that either something has gone wrong or those somehow represent insertions/deletions (gaps)
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-11T09:31:27.720Z
Comments.Text: can you try running with more iterations? Running with a single one makes little sense I think
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-12T17:44:29.287Z
Comments.Text: @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).
Comments.UserDisplayName: Aalawlx
Tags: <blast><sequence-homology><phylogenetics><pssm><psi-blast>
Title: What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?
ThreadText: # What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?
  
  (Asked by: username_0 on 2018-06-10)
  
  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
  
  ```
  
  **Tags:** blast, sequence-homology, phylogenetics, pssm, psi-blast
  
  > **Comments:**
  > **username_1**: I don't know but guess that either something has gone wrong or those somehow represent insertions/deletions (gaps)  
  > **username_1**: can you try running with more iterations? Running with a single one makes little sense I think  
  > **username_0**: @username_1 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).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-06-12. Score: 1 | Accepted answer
  
  It means -inf. It has to do with how the [PSSM](https://en.wikipedia.org/wiki/Position_weight_matrix) score is calculated.
  
  > **Comments:**
  > **username_1**: That sounds very plausible, do you have a source/reference? Aren't pseudocounts normally added by default? will running >1 iteration change this?  
  > **username_0**: 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.  
  > **username_2**: @username_1, if you have blast installed type in `psiblast -help`. You'll see that pseudocount is set by default to `0`.  
  > **username_1**: 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."  
  > **username_2**: @username_1, did you read `psiblast -help` or not? That is something else than a web interface.  
  
  ---
  
  