Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.
Nucleic Acids Res
; 43(7): 3442-53, 2015 Apr 20.
Article
em En
| MEDLINE
| ID: mdl-25779052
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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Pneumonia por Mycoplasma
/
Regiões Promotoras Genéticas
Tipo de estudo:
Clinical_trials
/
Prognostic_studies
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2015
Tipo de documento:
Article
País de afiliação:
Espanha