search_hmmsearch: Perform a hmmsearch search of a protein sequence against a...

In currocam/utilsHMMER: HMMERutils

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

Description

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

Usage

search_hmmsearch(aln, seqdb = "swissprot", timeout = 180, verbose = FALSE)

Arguments

aln	A Biostrings::AAMultipleAlignment or a list of Biostrings::AAMultipleAlignment.
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

system.file("extdata", "alignment.fasta", package = "HMMERutils") %>%
    Biostrings::readAAMultipleAlignment() %>%
    search_hmmsearch(
        seqdb = "swissprot",
        timeout = 180,
        verbose = FALSE
    )

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