R: Add a Sequence to an Existing Alignmnet

seq2aln {bio3d} | R Documentation

## 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", 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 `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.
`file` | name of ‘FASTA’ output file to which alignment should be written.
`...` | additional arguments passed to `seqaln`.

### 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.

### 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.

### Note

A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.

### Author(s)

Barry Grant

### 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

    ## Not run:
    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)

    ## End(Not run)

[Package bio3d version 2.3-3 Index]