search_hmmscan: Perform a hmmscan search of a protein sequence against a...

In currocam/HMMERutils: HMMERutils

Perform a hmmscan search of a protein sequence against a profile-HMM database.

Description

Perform a hmmscan search of a protein sequence against a profile-HMM database.

Usage

search_hmmscan(seq, hmmdb = "pfam", timeout = 180, verbose = FALSE)

Arguments

seq	A character vector containing the sequences of the query or any other object that can be converted to that. It can also be a URL or the path to a FASTA file.
hmmdb	A character vector containing the target databases. Frequently used databases are pfam, tigrfam gene3d, superfamily, pirsf and treefam, but a complete and updated list is available at https://www.ebi.ac.uk/Tools/hmmer/.
timeout	Set maximum request time in seconds.
verbose	A logical, if TRUE details of the download process is printed.

Value

An Data Frame containing the results from HMMER.

Examples

search_hmmscan(
    seq = "SWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSS",
    hmmdb = "pfam",
    verbose = FALSE
)

currocam/HMMERutils documentation built on Feb. 15, 2023, 8:41 p.m.