Mobile DNA

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.

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.

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.

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

LINE-1 ORF2p expression is nearly imperceptible in human cancers [Mob DNA 2019] PubMed

A benchmark of transposon insertion detection tools using real data [Mob DNA 2019] PubMed

Tools and best practices for retrotransposon analysis using high-throughput sequencing data [Mob DNA 2019] PubMed

A re-evaluation of LINE-1 ORF2 expression in LNCaP prostate cancer cells [Mob DNA 2019] PubMed

Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins [Nat Neurosci 2020] PubMed

View all editors' picks

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

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. 

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

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

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