ptm (version 0.2.2)

msa: Multiple Sequence Alignment

Description

Aligns multiple protein sequences.

Usage

msa(sequences, ids = names(sequences), sfile = FALSE, inhouse = FALSE)

Arguments

sequences

vector containing the sequences.

ids

vector containing the sequences' ids.

sfile

path to the file where the fasta alignment should be saved, if any.

inhouse

logical, if TRUE the in-house MUSCLE software is used. It must be installed on your system and in the search path for executables.

Value

Returns a list of four elements. The first one ($seq) provides the sequences analyzed, the second element ($ids) returns the identifiers, the third element ($aln) provides the alignment in fasta format and the fourth element ($ali) gives the alignment in matrix format.

References

Edgar RC. Nucl. Ac. Res. 2004 32:1792-1797.

Edgar RC. BMC Bioinformatics 5(1):113.

See Also

custom.aln(), list.hom(), parse.hssp(), get.hssp(), shannon()

Examples

# NOT RUN {
msa(sequences = sapply(c("P19446", "P40925", "P40926"), ptm::get.seq),
 ids = c("wmelon", "cyt", "mit"))
# }