bio3d (version 2.1-2)

hmmer: HMMER Sequence Search

Description

Run HMMER, against the PDB, NR, swissprot (and other) sequence databases.

Usage

hmmer(seq, type="phmmer", db = NULL, verbose = TRUE, timeout = 90)

Arguments

seq

a single element or multi-element character vector containing the query sequence. Alternatively a fasta object from function get.seq can be provided.

type

for now: phmmer, or hmmscan. Currently not available: hmmsearch, jackhmmer

db

a single element character vector specifying the database against which to search. Current options are pdb, nr and swissprot. More here...

verbose

logical, if TRUE details of the download process is printed.

timeout

integer specifying the number of seconds to wait for the blast reply before a time out occurs.

Value

• A data frame with the following components: this depends on the type.

Details

This function employs direct HTTP-encoded requests to the HMMER web server ...

Coppy from the HMMER website: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

References

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

Finn, R.D. et al. (2011) Nucl. Acids Res. 39, 29--37. Eddy, S.R. (2011) PLoS Comput Biol 7(10): e1002195. See also the HMMER website: http://hmmer.janelia.org

See Also

seqaln

Examples

##- PHMMER
seq <- get.seq("2abl_A", outfile=tempfile())
res <- hmmer(seq, db="pdb")

##- HMMSCAN
fam <- hmmer(seq, type="hmmscan", db="pfam")
pfam.aln <- pfam(fam$acc[1])

##- HMMSEARCH
hmm <- hmmer(pfam.aln, type="hmmsearch", db="pdb")
unique(hmm$species)
hmm$acc