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