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PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool
Tocquin, Pierre; Naomé, Aymeric; Jourdan, Samuel et al.
2016
 

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Abstract :
[en] In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.
Research center :
UR InBios - CIP
UR InBios - PhystoSYSTEMS
Disciplines :
Microbiology
Author, co-author :
Tocquin, Pierre  ;  Université de Liège > Département des sciences de la vie > Physiologie végétale
Naomé, Aymeric ;  Université de Liège > Département des sciences de la vie > Centre d'ingénierie des protéines
Jourdan, Samuel ;  Université de Liège > Département des sciences de la vie > Centre d'ingénierie des protéines
Anderssen, Sinaeda
Hiard, Samuel ;  Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Dép. d'électric., électron. et informat. (Inst.Montefiore)
van Wezel, Gilles
Hanikenne, Marc  ;  Université de Liège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale
Baurain, Denis  ;  Université de Liège > Département des sciences de la vie > Phylogénomique des eucaryotes
Rigali, Sébastien  ;  Université de Liège > Département des sciences de la vie > Département des sciences de la vie
Language :
English
Title :
PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool
Publication date :
01 November 2016
Publisher :
Cold Spring Harbor Labs Journals
Available on ORBi :
since 02 December 2016

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