bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.
Bioinformatics
; 33(3): 334-340, 2017 02 01.
Article
in En
| MEDLINE
| ID: mdl-27694198
ABSTRACT
Motivation The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ 70 promoters in Escherichia coli . Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli . Results:
Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σ A , σ C , σ H , σ G and σ F ) and for five classes of sigma factors in E. coli (σ 70 , σ 38 , σ 32 , σ 28 and σ 24 ). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F 1 -score = 0.93) compared to the next best tool with MCC = 0.59, F 1 -score = 0.79) and covers multiple classes of promoters. Availability and Implementation bTSSfinder is available standalone and online at http//www.cbrc.kaust.edu.sa/btssfinder . Contacts ilham.shahmuradov@kaust.edu.sa or vladimir.bajic@kaust.edu.sa. Supplementary information Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Promoter Regions, Genetic
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Cyanobacteria
/
Transcription Initiation Site
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Escherichia coli
Type of study:
Prognostic_studies
/
Risk_factors_studies
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2017
Type:
Article