Fast and accurate genome-scale identification of DNA-binding sites

David Martin 1 Vincent Maillol 1 Eric Rivals 2, 1
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Motivation: Discovering DNA binding sites in genome sequences is crucial for understanding genomic regulation. Currently available computational tools for finding binding sites with Position Weight Matrices of known motifs are often used in restricted genomic regions because of their long run times. The ever-increasing number of complete genome sequences points to the need for new generations of algorithms capable of processing large amounts of data. Results: Here we present MOTIF, a new algorithm for seeking transcription factor binding sites in whole genome sequences in a few seconds. We propose a web service that enables the users to search for their own matrix or for multiple JASPAR matrices. Beyond its efficacy , the service properly handles undetermined positions within the genome sequence and provides an adequate output listing for each position the matching word and its score. Availability: MOTIF is freely available for use through an interface at http://www. atgc-montpellier.fr/motif. The source code of the stand-alone search method of MOTIF is freely available at https://gite.lirmm.fr/rivals/motif.git. It is written in C++ and tested on Linux platforms.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01967466
Contributor : Eric Rivals <>
Submitted on : Monday, December 31, 2018 - 12:33:37 PM
Last modification on : Wednesday, July 10, 2019 - 10:40:45 AM
Long-term archiving on : Monday, April 1, 2019 - 12:41:38 PM

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David Martin, Vincent Maillol, Eric Rivals. Fast and accurate genome-scale identification of DNA-binding sites. BIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩. ⟨lirmm-01967466⟩

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