biopython v1.71.0 Bio.Align.AlignInfo.PSSM
Represent a position specific score matrix.
This class is meant to make it easy to access the info within a PSSM and also make it easy to print out the information in a nice table.
Let’s say you had an alignment like this::
GTATC AT--C CTGTC
The position specific score matrix (when printed) looks like::
G A T C G 1 1 0 1 T 0 0 3 0 A 1 1 0 0 T 0 0 2 0 C 0 0 0 3
You can access a single element of the PSSM using the following::
For instance, to get the ‘T’ residue for the second element in the above alignment you would need to do:
Link to this section Summary
Link to this section Functions
Initialize with pssm data to represent.
The pssm passed should be a list with the following structure:
list - The letter of the residue being represented (for instance, from the example above, the first few lists would be GTAT… list - A dictionary with the letter substitutions and counts.
Return the residue letter at the specified position.