seqaln.pair. bio3d 2.3-0

Usage

seqaln.pair(aln, ...)

Arguments

aln: a sequence character matrix, as obtained from seqbind, or an alignment list object as obtained from read.fasta.
...: additional arguments for the function seqaln.

Description

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

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.

Value

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

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


## NOTE: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED

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


##- Simple example
aln <- seqbind(c("X","C","X","X","A","G","K"),
               c("C","-","A","X","G","X","X","K"))

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

       1        10 
seq1   XCXXA-G--K
seq2   -C--AXGXXK
       ^*^^*^*^^* 
       1        10 

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

Class:
  fasta

Alignment dimensions:
  2 sequence rows; 10 position columns (4 non-gap, 6 gap) 

+ attr: id, ali, call

Author

Barry Grant

Sequence Alignment of Identical Protein Sequences