Download Pfam FASTA Sequence Alignment

Downloads FASTA sequence alignment from the Pfam database.

pfam(id, alignment = "seed", verbose = FALSE)

Arguments

id	the Pfam familiy identifier (e.g ‘Piwi’) or accession (e.g. ‘PF02171’).
alignment	the alignment type. Allowed values are: ‘seed’, ‘ncbi’, ‘full’, ‘metagenomics’.
verbose	logical, if TRUE details of the download process is printed.

Details

This is a basic function to download a multiple sequence alignment for a protein family from the Pfam database.

Value

A ‘fasta’ object with the following components:

ali

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

ids

sequence names as identifiers.

call

the matched call.

References

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

Author

Lars Skjaerven

Note

Full more information on the Pfam database:
http://pfam.xfam.org

See also

read.fasta, hmmer, get.seq, uniprot

Examples

if (FALSE) {
# PFAM server connection required - testing excluded

aln <- pfam("piwi")
aln <- pfam("PF02171")

seq <- get.seq("1rx2_A", outfile = tempfile())
hmm <- hmmer(seq, type="hmmscan", db="pfam")
aln <- pfam(hmm$hit.tbl$acc[1])

# Or much more simply for RCSB PDB entries:
acc <- pdb.pfam("1rx2_A", compact=FALSE)$pfamAcc
aln <- pfam(acc)
}