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LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

In this short report, the authors note how annotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. Even programs like LTR_FINDER, which are widely used  for the identification of LTR retrotransposons, can have their application on large genomes hindered by single-threaded processes. Here, the authors report an accessory program that allows parallel operation of LTR_FINDER.

Call for Papers: Endogenous Retroviruses in Evolution and Disease

The Editors of Mobile DNA and Retrovirology extend an invitation to submit original research articles related to endogenous retroviruses to their new collection: Endogenous Retroviruses in Evolution and Disease.

Open for submissions: May 24, 2019

Submit an article to Mobile DNA for the series.

Articles

  1. Authors: Daniel Ardeljan, Xuya Wang, Mehrnoosh Oghbaie, Martin S. Taylor, David Husband, Vikram Deshpande, Jared P. Steranka, Mikhail Gorbounov, Wan Rou Yang, Brandon Sie, H. Benjamin Larman, Hua Jiang, Kelly R. Molloy, Ilya Altukhov, Zhi Li, Wilson McKerrow…

    Content type: Research

Review collection
All Reviews
Repository for all published Review articles. Contributions from some of the leading researchers working with mobile DNA.

Article collection
Mobile DNA Tools
Repository for all published articles on softwares, databases, and methodologies.

2019
Thematic series

Endogenous Retroviruses in Evolution and Disease
Cross-journal series with Retrovirology. Edited by the Editors-in-Chief of Mobile DNA and Retrovirology.

Thematic series
Transposable Elements in Model Organisms (coming soon)
Edited by the Editors-in-Chief

2015
Thematic series
Keystone Symposium: Mobile Genetic Elements and Genome Evolution
Edited by: Henry Levin, Parmit Singh

2014
Review series

Mobile genetic elements in biotechnology
Edited by: Henry Levin, Thomas Eickbush, Marlene Belfort, Nancy Craig, Cedric Feschotte

2013
Review series

Mobile introns review series
Edited by: Thomas Eickbush, Marlene Belfort, Nancy Craig, Daniel Voytas

Pre-submission Inquiries

The Editors-in-Chief of Mobile DNA welcome authors to send any pre-submission inquiries they might have to the Editorial Email address, which can be found here by clicking on "Contact Us" (upper left side of page). We ask that you please include “Pre-submission inquiry” in the subject line of your email and that you include the title and abstract of your proposed submission within the message. Our Editors will do their best to respond to you in a timely manner.

Editors' Picks

Highlights from recent literature on mobile elements, selected by the Editors-in-Chief.

Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry [Mob DNA 2019] PubMed

Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA [Nucleic Acids Res 2019] PubMed

Completion of LINE integration involves an open '4-way' branched DNA intermediate [Nucleic Acids Res 2019] PubMed

Diversification of the Caenorhabditis heat shock response by Helitron transposable elements [Elife 2019] PubMed

Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development [Elife 2019] PubMed

View all editors' picks





Editors-in-Chief

Irina Arkhipova, Marine Biological Laboratory at Woods Hole
Cédric Feschotte, Cornell University
Haig Kazazian, Johns Hopkins University
Henry Levin, NIH

In 2019, we welcomed our new Associate Editors: 
Orsolya Barabas, European Molecular Biology Laboratory (EMBL), Germany
Gael Cristofari, Institut National de la Santé et de la Recherche Médicale, France 
Adam Ewing, Mater Research Institute-University of Queensland, Australia
Clément Gilbert, CNRS, Université Paris Saclay, France 
Molly G Hammell, Cold Spring Harbor Laboratory, USA
Damon R Lisch, Purdue University, USA
Joe Peters, Cornell University, USA
Phoebe Rice, The University of Chicago, USA

Aims and scope

Mobile DNA is an open access, peer-reviewed journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.

Latest Tweets

TE Digest

Updated monthly, check out the newest published research on transposable elements in the TE Digest on Alexander Suh of Uppsala University's Genomicrocosm page here

Links to Useful TE Community Resources

Transposable elements labs directory
Women in TEs (maintained by Cedric Feschotte)
Job vacancies
Transposons Worldwide SLACK Page (Managed by Rebecca Berrens)
Mobile DNA Tools Collection
TE digest (Managed by Alexander Suh)


Forthcoming meetings

3rd International Workshop on Human Endogenous Retroviruses & Diseases - November 5-6, 2019 - Lyon, FranceNew Content Item

4th International Congress on Transposable Elements - April 25-28, 2020 - Saint Malo, France

New Content Item​​​​​​​




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