PASTEC: an automatic transposable element classification tool.
CONCLUSIONS
The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus.


BACKGROUND
PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France; INRA, plateforme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées Toulouse UR875, Castanet-Tolosan, France.
Claire
C
Hoede
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France; INRA, LUNAM Université, Oniris, UMR1300 BioEpAR, Nantes, France.
Sandie
S
Arnoux
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France.
Mark
M
Moisset
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France.
Timothée
T
Chaumier
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France.
Olivier
O
Inizan
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France.
Véronique
V
Jamilloux
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France.
Hadi
H
Quesneville
D017360:Arabidopsis / Q000235:genetics; D001331:Automation; D004251:DNA Transposable Elements; D023281:Genomics / Q000379:methods*
D004251:DNA Transposable Elements