R/packFinder.R

In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

#' @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

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