bio3d (version 2.1-1)

seq2aln: 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", exefile = "muscle", 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 seq

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.

exefile

file path to the MUSCLE program on your system (i.e. how is MUSCLE invoked).

file

name of FASTA output file to which alignment should be written.

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.

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.

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

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)