Description Usage Arguments Details Value Author(s) See Also Examples
DNA/RNA Sequence Alignment for Two DNA/RNA Sequences
1 |
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 |
This function implements the sequence alignment between two DNA/RNA sequences.
An Biostrings object containing the scores and other alignment information.
Min-feng Zhu <wind2zhu@163.com>
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.
1 2 3 4 5 6 7 8 9 10 | # 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)
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