A package for the de novo discovery of Pack-TYPE transposons. Transposons are detected in DNA sequences based on conserved terminal inverted repeat sequences and presence of terminal site duplications. packFinder allows users to search a given Genome for Pack-TYPE transposons with minimal input and setup. For a more in-depth explanation, see our paper in PLOS Genetics.
packFinder is available from the Bioconductor project. With R >=4.0.0 installed, the following code can be used to install the package:
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("packFinder")
In order to use the functions packClust and packAlign, the VSEARCH command line tool must be installed. For Linux and MacOS systems, correct installation of VSEARCH should allow users to use all functions within packFinder; for windows users, the absolute path to the VSEARCH executable file must be specified when calling packFinder clustering and alignment functions. See the vignette, documentation or the VSEARCH github for further information.
Additionally, utilites are provided with the package for the functional annotation of internal transposon sequences using BLAST+; this application can be installed from NCBI.
The packFinder vignette includes a full walkthrough of the package. To get started quickly, it is easiest to download a genome of interest using the biomartr package and follow the steps outlined in the vignette.
If you use packFinder in your work, please cite the following publication:
Gisby, J. S. & Catoni, M. (2022) The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution. PLOS Genetics 18(2): e1010078.