seq2aln {bio3d}

Add a Sequence to an Existing Alignmnet

Description

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

Usage

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.

id

sequence names as identifers.

Note

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

Author(s)

Barry Grant

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/.

See Also

seqaln, read.fasta, read.fasta.pdb, seqbind

Examples

## Not run: 
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)

## End(Not run)