Sequence Alignment of Identical Protein Sequences
Create multiple alignments of amino acid sequences according to the method of Edgar.
seqaln.pair(aln, ...)
aln |
a sequence character matrix, as obtained from
|
... |
additional arguments for the function |
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.
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. |
A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.
Barry Grant
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: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED
if(check.utility("muscle")) {
##- 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())
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.