dfam.query: Query the Dfam database to annotate putative LTRs

View source: R/dfam.query.R

dfam.queryR Documentation

Query the Dfam database to annotate putative LTRs

Description

Validate or annotate putative LTR transposons that have been predicted using LTRharvest, LTRdigest, or LTRpred.

Usage

dfam.query(
  seq.file,
  Dfam.db = NULL,
  eval = 0.001,
  cores = 1,
  output.folder = getwd()
)

Arguments

seq.file

file path to the putative LTR transposon sequences in fasta format.

Dfam.db

folder path to the local Dfam database or Dfam.db = "download" in case the Dfam database shall be automatically downloaded before performing query analyses.

eval

E-value threshhold to perform the HMMer search against the Dfam database.

cores

number of cores to use to perform parallel computations.

output.folder

folder path to store the annotation results.

Details

The Dfam database provides a collection of curated transposable element annotations.

Author(s)

Hajk-Georg Drost


HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.