ORFpred: Open Reading Frame Prediction

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Open Reading Frame Prediction

Description

This function provides a wrapper to the USEARCH fastx_findorfs command line tool to predict ORFs in a given input fasta file and read the output as data.frame object.

Usage

ORFpred(
  seq.file,
  orf.style = 7,
  min.codons = 200,
  trans.seqs = FALSE,
  output = NULL
)

Arguments

seq.file	a fasta file storing the sequences for which open reading frames shall be predicted.
orf.style	type of predicting open reading frames (see documentation of USEARCH).
min.codons	minimum number of codons in the predicted open reading frame.
trans.seqs	logical value indicating wheter or not predicted open reading frames shall be translated and the corresponding protein sequences stored in the output folder.
output	path to the folder in which predicted open reading frame sequences shall be stored.

Author(s)

Hajk-Georg Drost

References

Robert Edgar. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 26 (19): 2460-2461.

See Also

LTRharvest, LTRdigest, LTRpred

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