BioMedR (version 1.2.1)

twoSeqSim: Protein/DNA Sequence Alignment for Two Protein Sequences

Description

Protein/DNA Sequence Alignment for Two Protein Sequences

Usage

twoSeqSim(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'.

Value

An Biostrings object containing the scores and other alignment information.

Details

This function implements the sequence alignment between two protein/DNA sequences.

See Also

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

Examples

# NOT RUN {
# Be careful when testing this since it involves sequence alignment
# and might produce unpredictable results in some environments

require(Biostrings)

s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
s2 = readFASTA(system.file('protseq/P10323.fasta', package = 'BioMedR'))[[1]]
seqalign = twoSeqSim(s1, s2)
summary(seqalign)
s11 = readFASTA(system.file('dnaseq/hs.fasta', package = 'BioMedR'))[[1]]
s21 = readFASTA(system.file('dnaseq/hs.fasta', package = 'BioMedR'))[[2]]
seqalign1 = twoSeqSim(s11, s21)
summary(seqalign1)
# }