Sequence Tools

This module defines functions and constants related to sequences.

prody.utilities.seqtools.alignBioPairwise(a_sequence, b_sequence, ALIGNMENT_METHOD='local', MATCH_SCORE=1.0, MISMATCH_SCORE=0.0, GAP_PENALTY=-1.0, GAP_EXT_PENALTY=-0.1, max_alignments=1)[source]

Wrapper function to align two sequences using Biopython to support deprecation and associated warnings.

It first attempts to use Bio.Align.PairwiseAligner and formats the output to match Bio.pairwise2 methods and if it doesn’t find it then it defaults back to Bio.pairwise2 methods.

Parameters:

  • a_sequence (str) – first sequence to align

  • b_sequence (str) – second sequence to align

  • ALIGNMENT_METHOD (str) – method for pairwise2 alignment Possible values are "local" and "global"

  • MATCH_SCORE (int) – a positive integer, used to reward finding a match

  • MISMATCH_SCORE (int) – a negative integer, used to penalise finding a mismatch

  • GAP_PENALTY (int) – a negative integer, used to penalise opening a gap

  • GAP_EXT_PENALTY (int) – a negative integer, used to penalise extending a gap

  • max_alignments (int) – maximum number of alignments to extract

prody.utilities.seqtools.splitSeqLabel(label)[source]

Returns label, starting residue number, and ending residue number parsed from sequence label.