CHAPS Help

Step 1: enter a set of accessions (one per line), or a set of fasta-formatted sequences; make sure you specify what you've entered in the Format: field.

Step 2: Click "Run ClustalW now"; the page should come back after a few seconds with a multiple alignment in the input box. You could have skipped Step 1 if you simply pasted in an already created multiple alignment, in "pseudo-ClustalW" format (i.e. just the alignment, no headers or footers).

Step 3: To generate the corresponding position-specific scoring matrix (PSSM or "profile"), click the "Generate PSSM now"; after a few seconds the PSSM field should be filled with the profile scoring matrix, followed by a second matrix indicating relative amino acid usage at each position, followed by two columns that provide the information content of the position and the fractional weight of the alignments, compared to pseudocounts.

Step 4: To use this profile in a PSI-BLAST seach, click the "Send to PSI-BLAST" button.

Optional step: To save either the multiple alignment, PSSM, or HMM to your local machine, press:
Download Multiple Alignment,
Download PSSM (ASN.1),
Download HMM.

These files can then be used for seaches with PSI-BLAST or HMM Search.

What are the numbers in the PSSM window?

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
    1 M   -1 -3 -3 -4  7 -2 -3 -3 -3  0  1 -2  5 -1 -3 -2 -1 -2 -2  0    0   0   0   0  44   0   0   0   0   0   0   0  56   0   0   0   0   0   0   0  0.66 0.09
    2 A    3 -1 -2 -1 -2  0  3 -2 -2 -1 -1 -1  4 -2 -2  0 -1 -3 -2 -1   41   0   0   0   0   0  31   0   0   0   0   0  29   0   0   0   0   0   0   0  0.32 0.15
    3 E   -1 -2 -1 -1 -3 -1  2  2 -2 -2 -2 -1  3 -3  4  1 -1 -3 -3 -2    0   0   0   0   0   0  18  18   0   0   0   0  20   0  25  19   0   0   0   0  0.45 0.18
    4 K   -1  0 -1 -1 -3  0 -1 -2 -2 -3 -3  3 -2 -4  6  1 -1 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0  36   0   0  45  19   0   0   0   0  0.91 0.18
    5 P   -2 -2 -3 -3 -3 -2 -2 -3 -1 -1  0 -2  5  0  5 -2 -2 -1  4 -1    0   0   0   0   0   0   0   0   0   0   0   0  40   0  36   0   0   0  25   0  0.75 0.18
    6 K   -1  0 -2 -2 -2 -1 -1 -3 -2  2 -1  3 -1 -2 -2 -1  2 -3 -2  2    0   0   0   0   0   0   0   0   0  20   0  36   0   0   0   0  25   0   0  19  0.27 0.18
    7 L   -2 -3 -4 -4 -2 -3 -3 -4 -4  1  4 -3  1  0 -3 -3 -1 -3 -2  2    0   0   0   0   0   0   0   0   0   0  75   0   0   0   0   0   0   0   0  25  0.57 0.18
    8 H   -1 -2 -1 -2 -3 -1 -2  4  6 -1 -2 -2 -2 -2 -3 -1 -2 -3 -1  1    0   0   0   0   0   0   0  40  36   0   0   0   0   0   0   0   0   0   0  25  0.53 0.18
    9 Y   -2 -2 -3 -4 -3 -2 -3 -4  1 -2 -2 -2 -2  3 -4 -2 -2  2  8 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0  1.25 0.18
   10 F   -3 -3 -4 -5 -3 -3 -4 -4 -2 -1 -1 -4 -1  6 -4 -3 -3  9  2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  60   0   0   0  40   0   0  1.38 0.18

The PSSM profile box is the output of the blastpgp -Q option. The left most 20 numbers are the scores that would be used in a similarity search. The next 20 numbers are the frequencies (percents) of each amino acid at that position. The last two floating point numbers are the information content at the position, and the relative weight of the multiple alignment data and the pseudocounts. If the last number is low, then BLOSUM62 is contributing most of the score information.