Sequence Analysis¶

This module contains features for analyzing protein sequences.

Classes¶

MSA - store MSA data indexed by label

Sequence - store sequence data

MSA IO¶

MSAFile - read/write MSA files in FASTA/SELEX/Stockholm formats

parseMSA() - parse MSA files

writeMSA() - parse MSA files

Editing¶

mergeMSA() - merge MSA data for multi-domain proteins

refineMSA() - refine MSA by removing gapped columns and/or sequences

Analysis¶

calcMSAOccupancy() - calculate row (sequence) or column occupancy

calcShannonEntropy() - calculate Shannon entropy

buildMutinfoMatrix() - build mutual information matrix

buildOMESMatrix() - build mutual observed minus expected squared covariance matrix

buildSCAMatrix()- build statistical coupling analysis matrix

buildSeqidMatrix()- build sequence identity matrix

buildDirectInfoMatrix() - build direct information matrix

uniqueSequences() - select unique sequences

applyMutinfoCorr() - apply correction to mutual information matrix

applyMutinfoNorm() - apply normalization to mutual information matrix

calcMeff() - calculate sequence weights

calcRankorder() - rank order scores

Plotting¶

showShannonEntropy() - plot Shannon entropy

showMSAOccupancy() - plot row (sequence) or column occupancy

showMutinfoMatrix() - show mutual information matrix