Download FASTA Sequence Files

Downloads FASTA sequence files from the NCBI nr, SWISSPROT/UNIPROT, OR RCSB PDB databases.

get.seq(ids, outfile = "seqs.fasta", db = "nr", verbose = FALSE)

Arguments

ids	A character vector of one or more appropriate database codes/identifiers of the files to be downloaded.
outfile	A single element character vector specifying the name of the local file to which sequences will be written.
db	A single element character vector specifying the database from which sequences are to be obtained.
verbose	logical, if TRUE URL details of the download process are printed.

Details

This is a basic function to automate sequence file download from the databases including NCBI nr, SWISSPROT/UNIPROT, and RCSB PDB.

Value

If all files are successfully downloaded a list object with two components is returned:

ali

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

ids

sequence names as identifiers.

This is similar to that returned by read.fasta. However, if some files were not successfully downloaded then a vector detailing which ids were not found is returned.

References

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

Author

Barry Grant

Note

For a description of FASTA format see: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml. When reading alignment files, the dash ‘-’ is interpreted as the gap character.

Examples

if (FALSE) {
## Sequence identifiers (GI or PDB codes e.g. from blast.pdb etc.)
get.seq( c("P01112", "Q61411", "P20171") )

#aa <-get.seq( c("4q21", "5p21") )
#aa$id
#aa$ali
}