bio3d (version 2.3-4)

as.fasta: Alignment to FASTA object

Description

Convert alignment/sequence in matrix/vector format to FASTA object.

Usage

as.fasta(x, id=NULL, …)

Arguments

x

a sequence character matrix/vector (e.g obtained from get.seq or seqbind).

id

a vector of sequence names to serve as sequence identifers. By default the function will use the row names of the alignment if they exists, otherwise ids will be generated.

…

arguments passed to and from functions.

Value

Returns a list of class "fasta" with the following components:

ali

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

id

sequence names as identifers.

call

the matched call.

Details

This function provides basic functionality to convert a sequence character matrix/vector to a FASTA object.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

get.seq, seqaln, seqbind, pdbaln

Examples

# NOT RUN {
as.fasta(c("A", "C", "D"))
# }