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