bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.
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 .



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.



bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder .



ilham.shahmuradov@kaust.edu.sa or vladimir.bajic@kaust.edu.sa.



Supplementary data are available at Bioinformatics online.
Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Ilham Ayub
IA
Shahmuradov
Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Rozaimi
R
Mohamad Razali
Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Salim
S
Bougouffa
Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Aleksandar
A
Radovanovic
Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Vladimir B
VB
Bajic
D000458:Cyanobacteria / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000378:metabolism; D012984:Software; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D015533:Transcriptional Activation
D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases
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