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.

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].