Module msa

Multiple sequence alignment (MSA) algorithms.

Functions

list of str, numpy rank-2 int array central_star(sequences, algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
Align multiple protein sequences to one reference by fusing multiple pairwise alignments.

list of str, numpy rank-2 int array msa_general(sequences, residue_numbers=None, msa_algorithm='Central Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
General interface for multiple sequence alignments (MSA).

list of str, numpy rank-2 int array msa_residue_numbers(sequences, residue_numbers=None)
Align multiple sequences based on the residue numbering.

list of lists of int # msa_residue_skipping(strings=None, gaps=None)
Create the residue skipping data structure.

Variables

__package__ = 'lib.sequence_alignment'

Imports: float64, int16, zeros, sys, RelaxError, align_pairwise

Function Details

central_star(sequences, algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)

Align multiple protein sequences to one reference by fusing multiple pairwise alignments.

Parameters:

• sequences (list of str) - The list of residue sequences as one letter codes.
• algorithm (str) - The pairwise sequence alignment algorithm to use.
• matrix (str) - The substitution matrix to use.
• gap_open_penalty (float) - The penalty for introducing gaps, as a positive number.
• gap_extend_penalty (float) - The penalty for extending a gap, as a positive number.
• end_gap_open_penalty (float) - The optional penalty for opening a gap at the end of a sequence.
• end_gap_extend_penalty (float) - The optional penalty for extending a gap at the end of a sequence.

Returns: list of str, numpy rank-2 int array

The list of alignment strings and the gap matrix.

msa_general(sequences, residue_numbers=None, msa_algorithm='Central Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)

General interface for multiple sequence alignments (MSA).

This can be used to select between the following MSA algorithms:

• 'Central Star', to use the central_star() function.
• 'residue number', to use the msa_residue_numbers() function.

Parameters:

• sequences (list of str) - The list of residue sequences as one letter codes.
• residue_numbers (list of list of int) - The list of residue numbers for each sequence.
• msa_algorithm (str) - The multiple sequence alignment (MSA) algorithm to use.
• pairwise_algorithm (str) - The pairwise sequence alignment algorithm to use.
• matrix (str) - The substitution matrix to use.
• gap_open_penalty (float) - The penalty for introducing gaps, as a positive number.
• gap_extend_penalty (float) - The penalty for extending a gap, as a positive number.
• end_gap_open_penalty (float) - The optional penalty for opening a gap at the end of a sequence.
• end_gap_extend_penalty (float) - The optional penalty for extending a gap at the end of a sequence.

Returns: list of str, numpy rank-2 int array

The list of alignment strings and the gap matrix.

msa_residue_numbers(sequences, residue_numbers=None)

Align multiple sequences based on the residue numbering.

Parameters:

• sequences (list of str) - The list of residue sequences as one letter codes.
• residue_numbers (list of list of int) - The list of residue numbers for each sequence.

Returns: list of str, numpy rank-2 int array

The list of alignment strings and the gap matrix.

msa_residue_skipping(strings=None, gaps=None)

Create the residue skipping data structure.

Parameters:

• strings (list of str) - The list of alignment strings.
• gaps (numpy rank-2 int array) - The gap matrix.

Returns: list of lists of int #

The residue skipping data structure. The first dimension is the molecule and the second is the residue. As opposed to zero, a value of one means the residue should skipped.