On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1089/cmb.2017.0219 http://hdl.handle.net/11449/176325 |
Resumo: | 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. |
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Repositório Institucional da UNESP |
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On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Modelsprofile hidden Markov modelsretrotransposonstransposable elements.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.Department of Statistics Applied Maths and Computer Sciences UNESP-São Paulo State University, Avenida 24-A, 1515 Rio ClaroDepartment of Computer Sciences Institute of Biosciences UNESP-São Paulo State UniversityDepartment of Computer Sciences Institute of Mathematical and Computer Sciences USP - University of São PauloDepartment of Statistics Applied Maths and Computer Sciences UNESP-São Paulo State University, Avenida 24-A, 1515 Rio ClaroDepartment of Computer Sciences Institute of Biosciences UNESP-São Paulo State UniversityUniversidade Estadual Paulista (Unesp)Universidade de São Paulo (USP)Fischer, Carlos N. [UNESP]Campos, Victor De A. [UNESP]Barella, Victor H.2018-12-11T17:20:08Z2018-12-11T17:20:08Z2018-05-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article517-527http://dx.doi.org/10.1089/cmb.2017.0219Journal of Computational Biology, v. 25, n. 5, p. 517-527, 2018.1066-5277http://hdl.handle.net/11449/17632510.1089/cmb.2017.02192-s2.0-85046884932Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Computational Biology0,824info:eu-repo/semantics/openAccess2021-10-23T17:16:52Zoai:repositorio.unesp.br:11449/176325Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T22:56:22.717437Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
title |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
spellingShingle |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models Fischer, Carlos N. [UNESP] profile hidden Markov models retrotransposons transposable elements. |
title_short |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
title_full |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
title_fullStr |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
title_full_unstemmed |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
title_sort |
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models |
author |
Fischer, Carlos N. [UNESP] |
author_facet |
Fischer, Carlos N. [UNESP] Campos, Victor De A. [UNESP] Barella, Victor H. |
author_role |
author |
author2 |
Campos, Victor De A. [UNESP] Barella, Victor H. |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade de São Paulo (USP) |
dc.contributor.author.fl_str_mv |
Fischer, Carlos N. [UNESP] Campos, Victor De A. [UNESP] Barella, Victor H. |
dc.subject.por.fl_str_mv |
profile hidden Markov models retrotransposons transposable elements. |
topic |
profile hidden Markov models retrotransposons transposable elements. |
description |
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. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T17:20:08Z 2018-12-11T17:20:08Z 2018-05-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
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 |
url |
http://dx.doi.org/10.1089/cmb.2017.0219 http://hdl.handle.net/11449/176325 |
identifier_str_mv |
Journal of Computational Biology, v. 25, n. 5, p. 517-527, 2018. 1066-5277 10.1089/cmb.2017.0219 2-s2.0-85046884932 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Computational Biology 0,824 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
517-527 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129476440096768 |