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Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes

Alexandru Al. Ecovoiu, Iulian Cristian Ghita, David Ioan Mihail Chifiriuc, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca, Alexandru Marian Bologa, Attila Cristian Ratiu
doi: https://doi.org/10.1101/2020.10.30.360610
Alexandru Al. Ecovoiu
1Department of Genetics, Faculty of Biology, University of Bucharest, Romania
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  • For correspondence: alexandru.ecovoiu@bio.unibuc.ro
Iulian Cristian Ghita
1Department of Genetics, Faculty of Biology, University of Bucharest, Romania
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David Ioan Mihail Chifiriuc
1Department of Genetics, Faculty of Biology, University of Bucharest, Romania
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Iulian Constantin Ghionoiu
3Accelerate Systems, London, UK
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Andrei Mihai Ciuca
2Exenne Technologies SRL, Bucharest, Romania
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Alexandru Marian Bologa
1Department of Genetics, Faculty of Biology, University of Bucharest, Romania
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Attila Cristian Ratiu
1Department of Genetics, Faculty of Biology, University of Bucharest, Romania
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Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 01, 2020.
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Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes
Alexandru Al. Ecovoiu, Iulian Cristian Ghita, David Ioan Mihail Chifiriuc, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca, Alexandru Marian Bologa, Attila Cristian Ratiu
bioRxiv 2020.10.30.360610; doi: https://doi.org/10.1101/2020.10.30.360610
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Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes
Alexandru Al. Ecovoiu, Iulian Cristian Ghita, David Ioan Mihail Chifiriuc, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca, Alexandru Marian Bologa, Attila Cristian Ratiu
bioRxiv 2020.10.30.360610; doi: https://doi.org/10.1101/2020.10.30.360610

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