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
Initialize with pssm data to represent
Return the residue letter at the specified position
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.