% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/repbase.query.R
\name{repbase.query}
\alias{repbase.query}
\title{Query the RepBase to annotate putative LTRs}
\usage{
repbase.query(
  seq.file,
  repbase.path,
  output = "RepbaseOutput.txt",
  max.hits = 5000,
  eval = 1e-30,
  cores = 1
)
}
\arguments{
\item{seq.file}{file path to the putative LTR transposon sequences in \code{fasta} format.}

\item{repbase.path}{file path to the RepBase file in \code{fasta} format.}

\item{output}{file name of the BLAST output.}

\item{max.hits}{maximum number of hits that shall be retrieved that still fulfill the e-value criterium.
Default is \code{max.hits = 5000}.}

\item{eval}{e-value threshold for BLAST hit detection. Default is \code{eval = 1E-30}.}

\item{cores}{number of cores to use to perform parallel computations.}
}
\description{
Validate or annotate putative LTR
transposons that have been predicted using LTRharvest or LTRdigest.
}
\details{
The RepBase database provides a collection of curated transposable element annotations.

This function allows users to validate or annotate putative LTR
transposons that have been predicted using LTRharvest or LTRdigest by blasting predicted LTR transposons 
to transposons known (annotated) in other species (e.g. such as Arabidopsis thaliana).

Internally, this function performs a \code{blastn} search of the putative LTR transposons predicted
by LTRharvest or LTRdigest against the Repbase fasta file that is specified by the user.

For this purpose it is required that the user has a working version of BLAST+ running on his or her machine.
}
\examples{
\dontrun{
# Example annotation run against the A thaliana RepBase using 4 cores
q <- repbase.query(seq.file     = "path/to/LTRtransposonSeqs.fasta",
                  repbase.path = "path/to/Athaliana_repbase.ref",
                  cores        = 4)
                 
Annot <- dplyr::select(dplyr::filter(dplyr::group_by(q,query_id), 
                                    (bit_score == max(bit_score))),
                                     query_id:q_len,evalue,bit_score,scope)
# select only hits with a scope > 0.1
Annot.HighMatches <- dplyr::filter(Annot, scope >= 0.1)
# Annotate the proportion of hits
barplot(sort(table(unlist(lapply(stringr::str_split(
        names(table(Annot.HighMatches$subject_id)),"_"), 
        function(x) x[2]))), decreasing = TRUE))
}
}
\references{
http://www.girinst.org/repbase/

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

Gish, W. & States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.

Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.

Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.

Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.
}
\author{
Hajk-Georg Drost
}
