calcTwoProtSeqSim {Rcpi} | R Documentation

## Protein Sequence Alignment for Two Protein Sequences

### Description

Protein Sequence Alignment for Two Protein Sequences

### Usage

    calcTwoProtSeqSim(seq1, seq2, type = "local", submat = "BLOSUM62")

### Arguments

`seq1` | A character string, containing one protein sequence.
`seq2` | A character string, containing another protein sequence.
`type` | Type of alignment, default is `'local'`, could be `'global'` or `'local'`, where `'global'` represents Needleman-Wunsch global alignment; `'local'` represents Smith-Waterman local alignment.
`submat` | Substitution matrix, default is `'BLOSUM62'`, could be one of `'BLOSUM45'`, `'BLOSUM50'`, `'BLOSUM62'`, `'BLOSUM80'`, `'BLOSUM100'`, `'PAM30'`, `'PAM40'`, `'PAM70'`, `'PAM120'`, `'PAM250'`.

### Details

This function implements the sequence alignment between two protein sequences.

### Value

An Biostrings object containing the scores and other alignment information.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

See `calcParProtSeqSim` for paralleled pairwise protein similarity calculation based on sequence alignment. See `calcTwoProtGOSim` for calculating the GO semantic similarity between two groups of GO terms or two Entrez gene IDs.

### Examples

    s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
    s2 = readFASTA(system.file('protseq/P10323.fasta', package = 'Rcpi'))[[1]]

    seqalign = calcTwoProtSeqSim(s1, s2)
    seqalign
    slot(seqalign, "score")

[Package Rcpi version 1.20.1 Index]