| seq2aln {bio3d} | R Documentation |
Add one or more sequences to an existing multiple alignment that you wish to keep intact.
seq2aln(seq2add, aln, id = "seq", exepath = "", file = "aln.fa")
seq2add |
an sequence character vector or an alignment list
object with id and ali components, similar to that
generated by read.fasta and seqaln. |
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. |
exepath |
path to the ‘MUSCLE’ program on your system (i.e. the directory where ‘MUSCLE’ is stored). |
file |
name of ‘FASTA’ output file to which alignment should be written. |
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.
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.
seqaln, read.fasta,
read.fasta.pdb, seqbind
## Not run:
aa.1 <- seq.pdb( read.pdb("1bg2") )
aa.2 <- seq.pdb( read.pdb("3dc4") )
aa.3 <- seq.pdb( read.pdb("1mkj") )
aln <- seqaln( seqbind(aa.1,aa.2) )
seq2aln(aa.3, aln)
## End(Not run)