Query the Dfam database to annotate putative LTRs

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

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.

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

Hajk-Georg Drost