twoSeqSim {rDNAse} | R Documentation |
DNA/RNA Sequence Alignment for Two DNA/RNA 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 |
submat |
Substitution matrix, default is |
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 <wind2zhu@163.com>
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)