Download Pfam FASTA Sequence Alignment
Downloads FASTA sequence alignment from the Pfam database.
pfam(id, alignment = "seed", verbose = FALSE)
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. |
This is a basic function to download a multiple sequence alignment for a protein family from the Pfam database.
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. |
Full more information on the Pfam database:
http://pfam.xfam.org
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Not run:
# 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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.