twoSeqSim: Protein/DNA Sequence Alignment for Two Protein Sequences

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

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'.

Details

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

Value

An Biostrings object containing the scores and other alignment information.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://nanx.me>

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

# 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)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.