LTR分类器：一个用于快速对植物中结构LTR逆转座子进行分类的网站。
LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.
作者信息
Monat Cecile, Tando Ndomassi, Tranchant-Dubreuil Christine, Sabot Francois
机构信息
UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.
出版信息
Mob Genet Elements. 2016 Sep 26;6(6):e1241050. doi: 10.1080/2159256X.2016.1241050. eCollection 2016.
Abstract
Automatic classification of LTR retrotransposons is a big challenge in the area of massive genomics. Many tools were developed to detect them but automatic classification is somehow challenging. Here we propose a simple approach, , based on recognition followed by analyses () to classify plant LTR retrotransposons in their respective superfamily, and () to provide automatically a basic functional annotation of these elements. The method was tested on various TE databases, and shown to be robust and fast. This tool is available as a web service implemented at IRD bioinformatics facility, http://LTRclassifier.ird.fr/.
摘要
长末端重复序列（LTR）逆转录转座子的自动分类是大规模基因组学领域的一项重大挑战。人们开发了许多工具来检测它们，但自动分类在某种程度上具有挑战性。在此，我们提出一种简单的方法，该方法基于识别，随后进行分析，以将植物LTR逆转录转座子分类到它们各自的超家族中，并自动提供这些元件的基本功能注释。该方法在各种转座元件（TE）数据库上进行了测试，结果表明它既稳健又快速。此工具作为一项网络服务，在法国国家农业研究院（IRD）生物信息学设施网站http://LTRclassifier.ird.fr/ 上提供。
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1
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Mob DNA. 2015 Jun 2;6:11. doi: 10.1186/s13100-015-0041-9. eCollection 2015.
2
PASTEC: an automatic transposable element classification tool.PASTEC：一种自动转座元件分类工具。
PLoS One. 2014 May 2;9(5):e91929. doi: 10.1371/journal.pone.0091929. eCollection 2014.
3
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.LTRsift：一种用于从头检测到的 LTR 反转录转座子的半自动分类和后处理的图形用户界面。
Mob DNA. 2012 Nov 7;3(1):18. doi: 10.1186/1759-8753-3-18.
4
Considering transposable element diversification in de novo annotation approaches.考虑从头注释方法中转座元件的多样化。
PLoS One. 2011 Jan 31;6(1):e16526. doi: 10.1371/journal.pone.0016526.
5
Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.使用 REPCLASS 探索重复 DNA 景观，这是一种自动化分类真核生物基因组中转座元件的工具。
Genome Biol Evol. 2009 Jul 23;1:205-20. doi: 10.1093/gbe/evp023.
6
Fine-grained annotation and classification of de novo predicted LTR retrotransposons.从头预测的长末端重复序列转座子的细粒度标注和分类。
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7
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8
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9
A unified classification system for eukaryotic transposable elements.真核生物转座元件的统一分类系统。
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