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On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models

Identificadores del recurso

http://dx.doi.org/10.1089/cmb.2017.0219

Journal of Computational Biology, v. 25, n. 5, p. 517-527, 2018.

1066-5277

http://hdl.handle.net/11449/176325

10.1089/cmb.2017.0219

2-s2.0-85046884932

Procedencia

(LA Referencia)

Ficha

Título:: On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models
Tema:: profile hidden Markov models; retrotransposons; transposable elements.
Descripción:: Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class. We compared the pHMMs of all six protocols. The test results show that, for each TE superfamily, the pHMMs of at least two of the proposed protocols performed better than the conventional one and that the number of correct predictions provided by the latter can be improved by considering together the results of one or more of the alternative protocols.
Fuente:: reponame:Repositório Institucional da UNESP; instname:Universidade Estadual Paulista (UNESP); instacron:UNESP
Idioma:: English
Relación:: Journal of Computational Biology; 0,824
Autor/Productor:: Fischer, Carlos N.; Campos, Victor De A.; Barella, Victor H.
Otros colaboradores/productores:: Universidade Estadual Paulista (UNESP)
Derechos:: info:eu-repo/semantics/openAccess
Fecha:: 2018-12-11T17:20:08Z; 2018-05-01
Tipo de recurso:: info:eu-repo/semantics/article; info:eu-repo/semantics/publishedVersion
Formato:: 517-527
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