R: Download FASTA Sequence Files

get.seq {bio3d} | R Documentation

## Download FASTA Sequence Files

### Description

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

### Usage

    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.

### 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.

### Author(s)

Barry Grant

### References

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

### See Also

`blast.pdb`, `read.fasta`, `read.fasta.pdb`, `get.pdb`

### Examples

    ## Not run:
    ## 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

    ## End(Not run)

[Package bio3d version 2.4-0 Index]