PASTEC: an automatic transposable element classification tool.
SUMMARY: 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...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4008368?pdf=render |
| _version_ | 1819263736421023744 |
|---|---|
| author | Claire Hoede Sandie Arnoux Mark Moisset Timothée Chaumier Olivier Inizan Véronique Jamilloux Hadi Quesneville |
| author_facet | Claire Hoede Sandie Arnoux Mark Moisset Timothée Chaumier Olivier Inizan Véronique Jamilloux Hadi Quesneville |
| author_sort | Claire Hoede |
| collection | DOAJ |
| description | SUMMARY: 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. AVAILABILITY: 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. |
| first_indexed | 2024-12-23T20:18:20Z |
| format | Article |
| id | doaj.art-22afb21e5ed040ed9e0b958beebfa5bc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T20:18:20Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-22afb21e5ed040ed9e0b958beebfa5bc2022-12-21T17:32:36ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0195e9192910.1371/journal.pone.0091929PASTEC: an automatic transposable element classification tool.Claire HoedeSandie ArnouxMark MoissetTimothée ChaumierOlivier InizanVéronique JamillouxHadi QuesnevilleSUMMARY: 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. AVAILABILITY: 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.http://europepmc.org/articles/PMC4008368?pdf=render |
| spellingShingle | Claire Hoede Sandie Arnoux Mark Moisset Timothée Chaumier Olivier Inizan Véronique Jamilloux Hadi Quesneville PASTEC: an automatic transposable element classification tool. PLoS ONE |
| title | PASTEC: an automatic transposable element classification tool. |
| title_full | PASTEC: an automatic transposable element classification tool. |
| title_fullStr | PASTEC: an automatic transposable element classification tool. |
| title_full_unstemmed | PASTEC: an automatic transposable element classification tool. |
| title_short | PASTEC: an automatic transposable element classification tool. |
| title_sort | pastec an automatic transposable element classification tool |
| url | http://europepmc.org/articles/PMC4008368?pdf=render |
| work_keys_str_mv | AT clairehoede pastecanautomatictransposableelementclassificationtool AT sandiearnoux pastecanautomatictransposableelementclassificationtool AT markmoisset pastecanautomatictransposableelementclassificationtool AT timotheechaumier pastecanautomatictransposableelementclassificationtool AT olivierinizan pastecanautomatictransposableelementclassificationtool AT veroniquejamilloux pastecanautomatictransposableelementclassificationtool AT hadiquesneville pastecanautomatictransposableelementclassificationtool |