Lloréns Rico, Verónica, 1989-Lluch-Senar, Maria 1982-Serrano Pubull, Luis, 1982-2015-11-172015-11-172015Lloréns-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):3442-53. DOI: 10.1093/nar/gkv1700305-1048http://hdl.handle.net/10230/25118Distinguishing 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.application/pdfeng© 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.Mycoplasma pneumoniae -- Aspectes genèticsMycoplasma pneumoniae -- MetabolismeGenomes bacteriansGenètica bacterianainfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/nar/gkv170info:eu-repo/semantics/openAccess