hmmSearch: Run hmmsearch (HMMER 3)

In iferres/dcda: Domain Content Dissimilarity Analysis

Description

Takes a fasta file and a Hidden Markov Model profile and performs a search of the former over the latter.

Usage

hmmSearch(bin, fasta, hmm, oty = "domtblout", cut = "ga", n_threads = 1L)

Arguments

bin	The location of hmmsearch binary.
fasta	A protein fasta file.
hmm	A hmm file. Must be pressed (see hmmpress from HMMER manual).
oty	The hmmsearch output type.
cut	One of "ga" or "tc". See HMMER 3.1b2 manual.
n_threads	An integer. The number of cores to use.

Value

The path to a temporary file where the hmmsearch output is placed.

iferres/dcda documentation built on May 31, 2019, 11:51 p.m.