T-lex2 : genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier)
Barrón Aduriz, Maite Garazi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Petrov, Dmitri A. (Department of Biology, Stanford University)
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))

Data:	2014
Resum:	Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge. net/projects/tlex.
Ajuts:	European Commission PCIG-GA-2011-293860 Ministerio de Economía y Competitividad BFU-2011-24397 Ministerio de Economía y Competitividad RYC-2010-07306
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	Nucleic acids research, Vol. 43 (december 2014) , p. e22, ISSN 1362-4962

DOI: 10.1093/nar/gku1250
PMID: 25510498

16 p, 3.7 MB

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