search_phmmer: Perform a phmmer search of a protein sequence against a...

In currocam/utilsHMMER: HMMERutils

Perform a phmmer search of a protein sequence against a protein sequence database.

Description

Perform a phmmer search of a protein sequence against a protein sequence database.

Usage

search_phmmer(seq, seqdb = "swissprot", 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.
seqdb	A character vector containing the target databases. Frequently used databases are swissprot, uniprotrefprot, uniprotkb, ensembl, pdb and alphafold, 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_phmmer(
    seq = "MTEITAAMVKELRTGAGMMDCKN",
    seqdb = "pdb",
    verbose = FALSE
)

currocam/utilsHMMER documentation built on Feb. 19, 2023, 9:54 p.m.