#' @title
#' packFinder: a package for the de novo Annotation
#' of Pack-TYPE Transposable Elements
#'
#' @description
#' Algorithm and tools for in silico pack-TYPE transposon
#' discovery. Filters a given genome for properties unique
#' to DNA transposons and provides tools for the
#' investigation of returned matches.
#'
#' @section Main Algorithm:
#' The goal of packFinder was to implement a simple
#' tool for the prediction of potential Pack-TYPE
#' elements. packFinder uses the following prior
#' knowledge, provided by the user, to detect transposons:
#'
#' \itemize{
#' \item Terminal Inverted Repeat (TIR) Base Sequence
#' \item Length of Terminal Site Duplication (TSD)
#' \item Length of the Transposon
#' }
#'
#' These features provide enough information to detect
#' autonomous and pack-TYPE elements. For a transposon
#' to be predicted by packFinder its TSD sequences
#' must be identical to each other, its forward TIR
#' sequence must match the base sequence provided and
#' its reverse TIR sequence must match its reverse complement.
#'
#' Transposons are therefore predicted by searching a
#' given genome for these characteristics, and further
#' analysis steps can reveal the nature of these elements
#' - while the packFinder tool is sensitive for the
#' detection of transposons, it does not discriminate
#' between autonomous and Pack-TYPE elements. Autonomous
#' elements will contain a transposase gene within the
#' terminal inverted repeats and tend to be larger than
#' their Pack-TYPE counterparts; pack-TYPE elements
#' instead capture sections of host genomes. Following
#' cluster analysis, BLAST can be used to discern
#' which predicted elements are autonomous
#' (transposase-containing) and with are true
#' Pack-TYPE elements.
#'
#' @section Workflow:
#' An example of a standard workflow can be found using
#' \code{browseVignettes(package = "packFinder")}. The
#' primary functions include:
#'
#' \itemize{
#' \item packSearch - the packSearch algorithm
#' uses simple pattern matching to detect
#' DNA transposons.
#' \item packClust - VSEARCH is used for
#' clustering elements based on sequence
#' similarity.
#' }
#'
#' Having obtained the sequences of transposable
#' elements in a given genome, it is recommende
#' to carry out a BLAST search for each transposon
#' cluster. This can identify which elements are
#' likely autonomous, and which may be Pack-TYPE.
#'
#' The \code{packFinder} functions report the
#' position of elements in a given genome using a
#' dataframe in the format of \code{\link{packMatches}}.
#' This dataframe is in the format produced by
#' coercing a \code{link[GenomicRanges:GRanges-class]{GRanges}}
#' object to a dataframe: \code{data.frame(GRanges)}.
#'
#' @name
#' packFinder
#'
#' @seealso
#' \code{\link{packSearch}}
#'
#' @author
#' Jack Gisby
NULL
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