text: user1606: 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
  
  
  user939: It means -inf. It has to do with how the PSSM score is calculated.
  
original_text: 1606: <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>
   939: <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>
  