as.fasta. bio3d 2.3-0

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.

Description

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

Details

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

Value

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.

References

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

Examples

as.fasta(c("A", "C", "D"))

       1 3 
seq1   ACD
       1 3 

Call:
  as.fasta(x = c("A", "C", "D"))

Class:
  fasta

Alignment dimensions:
  1 sequence rows; 3 position columns (3 non-gap, 0 gap) 

+ attr: id, ali, call

Author

Lars Skjaerven

Alignment to FASTA object