bTSSfinder

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

Ilham Ayub Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, Vladimir B. Bajic

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

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.

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 .

Original languageEnglish
Pages (from-to)334-340
Number of pages7
JournalBioinformatics (Oxford, England)
Volume33
Issue number3
DOIs
Publication statusPublished - 1 Feb 2017
Externally publishedYes

Fingerprint

Cyanobacteria
Promoter
Escherichia coli
Escherichia Coli
Sigma Factor
Computational Biology
Prediction
Bioinformatics
Bacterial Genomes
Genes
Transcription Initiation Site
Transcriptional Activation
Transcription
Chemical activation
Availability
Proteins
Activation
High Accuracy
Genome
Cover

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

bTSSfinder : a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. / Shahmuradov, Ilham Ayub; Mohamad Razali, Rozaimi; Bougouffa, Salim; Radovanovic, Aleksandar; Bajic, Vladimir B.

In: Bioinformatics (Oxford, England), Vol. 33, No. 3, 01.02.2017, p. 334-340.

Research output: Contribution to journalArticle

Shahmuradov, Ilham Ayub ; Mohamad Razali, Rozaimi ; Bougouffa, Salim ; Radovanovic, Aleksandar ; Bajic, Vladimir B. / bTSSfinder : a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. In: Bioinformatics (Oxford, England). 2017 ; Vol. 33, No. 3. pp. 334-340.
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