Combine Sequences by Rows Without Recycling

Usage

seqbind(..., blank = "-")

Arguments

...
vectors, matrices, and/or alignment ‘fasta’ objects to combine.
blank
a character to add to short arguments, to achieve the same length as the longer argument.

Description

Take vectors and/or matrices arguments and combine them row-wise without recycling them (as is the case with rbind).

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.

References

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

Examples

## Read two pdbs
a.pdb <- read.pdb("1bg2")



  Note: Accessing on-line PDB file



b.pdb <- read.pdb("1goj")



  Note: Accessing on-line PDB file




seqs <- seqbind(aa321(a.pdb$atom[a.pdb$calpha,"resid"]),
                aa321(b.pdb$atom[b.pdb$calpha,"resid"]))

# seqaln(seqs)

See also

seqaln, read.fasta, read.pdb, write.fasta, rbind

Author

Barry Grant