Package procope.methods.interologs

Interface Summary
InterologScorer Implemented by classes which calculate scores for homology-transferred interactions (interologs).
 

Class Summary
AlignmentInterologScorer Implements interolog scoring using similarity or identity from pairwise sequence alignments of the homologs.
EvalueInterologScorer Implements interolog scoring using the geometric mean of the two BLAST evalues involved in a transferred protein interaction (when transferred using bidirectional best hits from BLAST).
FASTAParser Reads sequences in (multi-)FASTA format.
InterologsCalculator Calculates interologs from a given set of binary interactions and a (homology) mapping between proteins.
Sequences A set of sequences internally represented by a internal_id=>sequence mapping.
 

Enum Summary
AlignmentInterologScorer.AlignmentScoring Defines the alignment measure which will be used