R/704-calcProtSeqSim.R
calcTwoProtSeqSim.Rd
Protein Sequence Alignment for Two Protein Sequences
calcTwoProtSeqSim(seq1, seq2, type = "local", submat = "BLOSUM62")
seq1 | A character string, containing one protein sequence. |
---|---|
seq2 | A character string, containing another protein sequence. |
type | Type of alignment, default is |
submat | Substitution matrix, default is |
An Biostrings object containing the scores and other alignment information.
This function implements the sequence alignment between two protein sequences.
See calcParProtSeqSim
for paralleled pairwise
protein similarity calculation based on sequence alignment.
See calcTwoProtGOSim
for calculating the
GO semantic similarity between two groups of GO terms or two Entrez gene IDs.
# NOT RUN { s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]] s2 = readFASTA(system.file('protseq/P10323.fasta', package = 'Rcpi'))[[1]] # }# NOT RUN { seqalign = calcTwoProtSeqSim(s1, s2) seqalign slot(seqalign, "score") # }