hmm_search: search profile(s) against a sequence database

In computational-genomics-lab/motifFUN: Searching user-defined motif along with functional annotation filtering criteria

Description

hmmsearch is used to search one or more profiles against a sequence database.

Usage

hmm_search(hmmsearch_path = NULL, seed = NULL, hmm.tresh = NULL,
  original.seq = NULL)

Arguments

hmmsearch_path	complete path of HMMER
seed	The seed to used with HMMER commands. Set this to get the same output each time.
hmm.tresh	Set the bit score cutoff for the per-sequence ranked hit list to a real number. (Default = 0)
original.seq	The absolute path for the original six-frame translation FASTA file

Value

Resulted output file name

@examples hmm_search(hmmsearch_path = NULL, seed = NULL,hmm.tresh = NULL, original.seq = NULL)

computational-genomics-lab/motifFUN documentation built on June 4, 2019, 7:52 a.m.