PREDetector: a new tool to identify regulatory elements in bacterial genomes

S. Hiard, R. Marée, S. Colson, P. Hoskisson, F. Titgemeyer, G. van Wezel, B. Joris, L. Wehenkel, S. Rigali

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

In the post-genomic area, the prediction of transcription factor regulons by position weight matrix-based programmes is a powerful approach to decipher biological pathways and to modelize regulatory networks in bacteria. The main difficulty once a regulon prediction is available is to estimate its reliability prior to start expensive experimental validations and therefore trying to find a way how to identify true positive hits from an endless list of potential target genes of a regulatory protein. Here we introduce PREDetector (Prokaryotic Regulatory Elements Detector), a tool developed for predicting regulons of DNA-binding proteins in bacterial genomes that, beside the automatic prediction, scoring and positioning of potential binding sites and their respective target genes in annotated bacterial genomes, it also provides an easy way to estimate the thresholds where to find reliable possible new target genes. PREDetector can be downloaded freely at http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php.
LanguageEnglish
Pages861-864
Number of pages3
JournalBiochemical and Biophysical Research Communications
Volume357
Issue number4
DOIs
Publication statusPublished - 2007

Fingerprint

Bacterial Genomes
Regulon
Genes
Detectors
Position-Specific Scoring Matrices
DNA-Binding Proteins
Regulator Genes
Transcription Factors
Binding Sites
Bacteria
Proteins

Keywords

  • regulon prediction
  • transcriptional regulation
  • regulatory networks
  • position weight matrix
  • DNA-binding motif

Cite this

Hiard, S. ; Marée, R. ; Colson, S. ; Hoskisson, P. ; Titgemeyer, F. ; van Wezel, G. ; Joris, B. ; Wehenkel, L. ; Rigali, S. / PREDetector: a new tool to identify regulatory elements in bacterial genomes. In: Biochemical and Biophysical Research Communications. 2007 ; Vol. 357, No. 4. pp. 861-864.
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Hiard, S, Marée, R, Colson, S, Hoskisson, P, Titgemeyer, F, van Wezel, G, Joris, B, Wehenkel, L & Rigali, S 2007, 'PREDetector: a new tool to identify regulatory elements in bacterial genomes' Biochemical and Biophysical Research Communications, vol. 357, no. 4, pp. 861-864. https://doi.org/10.1016/j.bbrc.2007.03.180

PREDetector: a new tool to identify regulatory elements in bacterial genomes. / Hiard, S.; Marée, R.; Colson, S.; Hoskisson, P.; Titgemeyer, F.; van Wezel, G.; Joris, B.; Wehenkel, L.; Rigali, S.

In: Biochemical and Biophysical Research Communications, Vol. 357, No. 4, 2007, p. 861-864.

Research output: Contribution to journalArticle

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AU - Hiard, S.

AU - Marée, R.

AU - Colson, S.

AU - Hoskisson, P.

AU - Titgemeyer, F.

AU - van Wezel, G.

AU - Joris, B.

AU - Wehenkel, L.

AU - Rigali, S.

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KW - regulon prediction

KW - transcriptional regulation

KW - regulatory networks

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