The twilight zone of cis element alignments

12 Pags., 8 Figs.

Detalles Bibliográficos
Autores: Sebastián Yagüe, Álvaro, Contreras-Moreira, Bruno
Tipo de recurso: artículo
Fecha de publicación:2013
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/65628
Acceso en línea:http://hdl.handle.net/10261/65628
Access Level:acceso abierto
id ES_2fa2960535a7aa0c19e99d038fb9d78a
oai_identifier_str oai:digital.csic.es:10261/65628
network_acronym_str ES
network_name_str España
repository_id_str
spelling The twilight zone of cis element alignmentsSebastián Yagüe, ÁlvaroContreras-Moreira, Bruno12 Pags., 8 Figs.Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.Funding for open access charge: Programa Euroinvestigación/Plant KBBE 2008 [EUI2008-03612].Peer reviewedOxford University Press2013info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/65628reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1093/nar/gks1301info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/656282026-05-22T06:33:51Z
dc.title.none.fl_str_mv The twilight zone of cis element alignments
title The twilight zone of cis element alignments
spellingShingle The twilight zone of cis element alignments
Sebastián Yagüe, Álvaro
title_short The twilight zone of cis element alignments
title_full The twilight zone of cis element alignments
title_fullStr The twilight zone of cis element alignments
title_full_unstemmed The twilight zone of cis element alignments
title_sort The twilight zone of cis element alignments
dc.creator.none.fl_str_mv Sebastián Yagüe, Álvaro
Contreras-Moreira, Bruno
author Sebastián Yagüe, Álvaro
author_facet Sebastián Yagüe, Álvaro
Contreras-Moreira, Bruno
author_role author
author2 Contreras-Moreira, Bruno
author2_role author
description 12 Pags., 8 Figs.
publishDate 2013
dc.date.none.fl_str_mv 2013
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/65628
url http://hdl.handle.net/10261/65628
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1093/nar/gks1301
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869405490977439744
score 15.811543

Similares en LA Referencia