% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ORFpred.R
\name{ORFpred}
\alias{ORFpred}
\title{Open Reading Frame Prediction}
\usage{
ORFpred(
  seq.file,
  orf.style = 7,
  min.codons = 200,
  trans.seqs = FALSE,
  output = NULL
)
}
\arguments{
\item{seq.file}{a fasta file storing the sequences for which open reading frames shall be predicted.}

\item{orf.style}{type of predicting open reading frames (see documentation of USEARCH).}

\item{min.codons}{minimum number of codons in the predicted open reading frame.}

\item{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.}

\item{output}{path to the folder in which predicted open reading frame sequences shall be stored.}
}
\description{
This function provides a wrapper to the \code{USEARCH}
\code{fastx_findorfs} command line tool to predict ORFs in
a given input fasta file and read the output as \code{\link{data.frame}} object.
}
\references{
Robert Edgar. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 26 (19): 2460-2461.
}
\seealso{
\code{\link{LTRharvest}}, \code{\link{LTRdigest}}, \code{\link{LTRpred}}
}
\author{
Hajk-Georg Drost
}
