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Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae

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dc.contributor.author Lloréns Rico, Verónica, 1989-
dc.contributor.author Lluch-Senar, Maria 1982-
dc.contributor.author Serrano Pubull, Luis, 1982-
dc.date.accessioned 2015-11-17T15:16:07Z
dc.date.available 2015-11-17T15:16:07Z
dc.date.issued 2015
dc.identifier.citation Lloréns-Rico V, Lluch-Senar M, Serrano L. Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae. Nucleic acids research. 2015; 43(7): 3442-3453. DOI 10.1093/nar/gkv170
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/25118
dc.description.abstract Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied the genome-reduced bacterium Mycoplasma pneumoniae, for which the RNAs associated with transcriptional start sites have been recently experimentally identified. We determined the contribution to transcription events of different genomic features: the -10, extended -10 and -35 boxes, the UP element, the bases surrounding the -10 box and the nearest-neighbor free energy of the promoter region. Using a random forest classifier and the aforementioned features transformed into scores, we could distinguish between true, abortive promoters and non-promoters with good -10 box sequences. The methods used in this characterization of promoters can be extended to other bacteria and have important applications for promoter design in bacterial genome engineering.
dc.description.sponsorship European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council [232913]; Fundación Botín, the Spanish Ministry of Economy and Competitiveness [BIO2007-61762]; National Plan of R + D + i; ISCIII – Subdirección General de Evaluación y Fomento de la Investigación [PI10/01702]; European Regional Development Fund (ERDF) (to the ICREA Research Professor L.S.]; Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 [SEV-2012-0208]. Funding for open access charge: European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council [232913]; Fundaci´on Bot´ın, the Spanish Ministry of Economy and Competitiveness [BIO2007-61762]; National Plan of R + D + i; ISCIII – Subdirección General de Evaluación y Fomento de la Investigación [PI10/01702]; European Regional Development Fund (ERDF) (to the ICREA Research Professor L.S.]; Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 [SEV-2012-0208].
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic acids research. 2015; 43(7): 3442-3453
dc.rights © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject.other Mycoplasma pneumoniae -- Aspectes genètics
dc.subject.other Mycoplasma pneumoniae -- Metabolisme
dc.subject.other Genomes bacterians
dc.subject.other Genètica bacteriana
dc.title Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkv170
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/232913
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-61762
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/acceptedVersion


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