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 1.4.0 Index]