bio3d (version 2.1-2)

seqaln.pair: Sequence Alignment of Identical Protein Sequences

Description

Create multiple alignments of amino acid sequences according to the method of Edgar.

Usage

seqaln.pair(aln, extra.args = "", ...)

Arguments

aln

a sequence character matrix, as obtained from seqbind, or an alignment list object as obtained from read.fasta.

extra.args

a single character string containing extra command line arguments for the alignment program.

...

additional arguments for the function seqaln.

Value

• A list with two components:
• ali
  an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
• ids
  sequence names as identifers.

Details

This function is intended for the alignment of identical sequences only. For standard alignment see the related function seqaln.

This function is useful for determining the equivalences between sequences and structures. For example in aligning a PDB sequence to an existing multiple sequence alignment, where one would first mask the alignment sequences and then run the alignment to determine equivalences.

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

## NOTE: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED
if(check.utility("muscle")) {

##- Aligning a PDB sequence to an existing sequence alignment


##- Simple example
aln <- list(ali=seqbind(c("X","C","X","X","A","G","K"),
                        c("C","-","A","X","G","X","X","K")),
            id=c("a","b"))

seqaln.pair(aln, outfile = tempfile())

}