biopython

v1.71.0

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::

your_pssm[sequence_number][residue_count_name]

For instance, to get the ‘T’ residue for the second element in the above alignment you would need to do:

your_pssm[1][‘T’]

Link to this section Summary

Functions

__init__()

Initialize with pssm data to represent

get_residue()

Return the residue letter at the specified position

Link to this section Functions

Link to this function __init__()

Initialize with pssm data to represent.

The pssm passed should be a list with the following structure:

list[0] - The letter of the residue being represented (for instance, from the example above, the first few list[0]s would be GTAT… list[1] - A dictionary with the letter substitutions and counts.

Link to this function get_residue()

Return the residue letter at the specified position.