orfSimilarity {GeneStructureTools}R Documentation

calculate percentage of orfB contained in orfA

Description

calculate percentage of orfB contained in orfA

Usage

orfSimilarity(orfA, orfB, substitutionCost = 100)

Arguments

orfA

character string of ORF amino acid sequence

orfB

character string of ORF amino acid sequence

substitutionCost

cost for substitutions in ORF sequences. Set to 1 if substitutions should be weighted equally to insertions and deletions.

Value

percentage of orfB contained in orfA

Author(s)

Beth Signal

See Also

Other ORF annotation: getOrfs, getUOrfs, maxLocation

Examples

orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAFRQFSLT")
orfSimilarity("MFGLDIYAFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFSLT","MFGLDIYAGTRSSFRQFSLT", 1)
[Package GeneStructureTools version 1.6.0 Index]