Add a Sequence to an Existing Alignmnet

Add one or more sequences to an existing multiple alignment that you wish to keep intact.

seq2aln(seq2add, aln, id = "seq", file = "aln.fa", ...)

Arguments

seq2add	an sequence character vector or an alignment list object with `id` and `ali` components, similar to that generated by `read.fasta` and `seqaln`.
aln	an alignment list object with `id` and `ali` components, similar to that generated by `read.fasta` and `seqaln`.
id	a vector of sequence names to serve as sequence identifers.
file	name of ‘FASTA’ output file to which alignment should be written.
...	additional arguments passed to `seqaln`.

Details

This function calls the ‘MUSCLE’ program, to perform a profile profile alignment, which MUST BE INSTALLED on your system and in the search path for executables.

Value

A list with two components:

ali

an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.

sequence names as identifers.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

‘MUSCLE’ is the work of Edgar: Edgar (2004) Nuc. Acid. Res. 32, 1792--1797.

Full details of the ‘MUSCLE’ algorithm, along with download and installation instructions can be obtained from:
http://www.drive5.com/muscle.

Author

Barry Grant

Note

A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.

Examples


if (FALSE) {
aa.1 <- pdbseq( read.pdb("1bg2") )
aa.2 <- pdbseq( read.pdb("3dc4") )
aa.3 <- pdbseq( read.pdb("1mkj") )

aln <- seqaln( seqbind(aa.1,aa.2) )

seq2aln(aa.3, aln)
}