Add one or more sequences to an existing multiple alignment that you wish to keep intact.
seq2aln(seq2add, aln, id = "seq", file = "aln.fa", ...)A list with two components:
an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
sequence names as identifers.
an sequence character vector or an alignment list
object with id and ali components, similar to that
generated by read.fasta and seqaln.
an alignment list object with id and ali
components, similar to that generated by read.fasta
and seqaln.
a vector of sequence names to serve as sequence identifers.
name of ‘FASTA’ output file to which alignment should be written.
additional arguments passed to seqaln.
Barry Grant
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.
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/.
seqaln, read.fasta,
read.fasta.pdb, seqbind
if (FALSE) {
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)
}
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