twoSeqSim: DNA/RNA Sequence Alignment for Two DNA/RNA Sequences

In wind22zhu/rDNAse: R package for generating various numerical representation schemes of DNA sequences.

Description

DNA/RNA Sequence Alignment for Two DNA/RNA Sequences

Usage

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

Arguments

seq1	A character string, containing one DNA/RNA sequence.
seq2	A character string, containing another DNA/RNA 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 DNA/RNA sequences.

Value

An Biostrings object containing the scores and other alignment information.

Author(s)

Min-feng Zhu <[e-mail]>

See Also

See parSeqSim for paralleled pairwise DNA/RNA 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('dnaseq/hs.fasta', package = 'rDNA'))[[1]]
s2 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[2]]
seqalign = twoSeqSim(s1, s2)
summary(seqalign)
print(seqalign@score)

wind22zhu/rDNAse documentation built on May 4, 2019, 6:31 a.m.