RT Journal Article
SR Electronic
T1 Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.10.30.360610
DO 10.1101/2020.10.30.360610
A1 Alexandru Al. Ecovoiu
A1 Iulian Cristian Ghita
A1 David Ioan Mihail Chifiriuc
A1 Iulian Constantin Ghionoiu
A1 Andrei Mihai Ciuca
A1 Alexandru Marian Bologa
A1 Attila Cristian Ratiu
YR 2020
UL http://biorxiv.org/content/early/2020/11/01/2020.10.30.360610.abstract
AB Transposon annotation is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor were reported. Genome ARTIST (GA) software was initially developed for mapping artificial transposons mobilized during insertional mutagenesis projects. Now, the new functions of GA_v2 qualify it as an effective companion for mapping and annotation of class II natural transposons in assembled genomes, contigs or sequencing reads.Tabular export of mapping and annotation data for subsequent high-throughput data analysis, the export of a list of flanking sequences around either the coordinates of insertion or around the target site duplications (TSDs) and generation of a consensus sequence for the respective flanking sequences are all key assets of GA_v2.Additionally, we developed two accompanying short scripts that enable the user to annotate transposons existent in assembled genomes and to use various annotation offered by FlyBase for Drosophila melanogaster genome.Herein, we present the applicability of GA_v2 for a preliminary annotation of the class II transposon P-element in the genome of D. melanogaster strain Horezu, Romania, which was sequenced with Nanopore technology in our laboratory. Our results point that GA_v2 is a reliable tool to be integrated in pipelines designed to perform transposon annotation in new sequenced genomes.GA_v2 is open source software compatible with Ubuntu, Mac OS and Windows and is available at https://github.com/genomeartist/genomeartist and at www.genomeartist.ro.Competing Interest StatementThe authors have declared no competing interest.