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Comparaison des cibles d’une matrice de score et d’une expression régulière. Application à la recherche de sites de fixation du facteur de transcription LXR

Abstract : In bioinformatics, it is a common task to search for new instances of a pattern built from a set of reference sequences. For the simplest and most frequent cases, patterns are represented in two ways : regular expression or scoring matrix. In the first case, the acceptance of a sequence is a binary decision. In the second case, the quality of the sequence is indicated by a score. Since both representations seem to be used indifferently in pratice, one may wonder if they have any impact on the result. Is there a best representation? What is the accurate threshold value for a scoring matrix? Allowing mutations in a regular expression is it comparable to moving the score of acceptance of a matrix? These are questions adressed in this paper, through a test case on binding site search. This study compares hits obtained with scoring matrices or by regular expressions allowing up to two substitutions. The study shows that, in our LXR study, sequences found by a scoring matrix are closer to the targeted hits than sequences found by a regular expression.
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https://hal.inria.fr/hal-01197050
Contributor : Catherine Belleannée <>
Submitted on : Friday, September 11, 2015 - 8:49:22 AM
Last modification on : Friday, July 10, 2020 - 4:18:04 PM
Long-term archiving on: : Tuesday, December 29, 2015 - 12:15:58 AM

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  • HAL Id : hal-01197050, version 1
  • PRODINRA : 325036

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Aymeric Antoine-Lorquin, Sandrine Lagarrigue, Frédéric Lecerf, Jacques Nicolas, Catherine Belleannée. Comparaison des cibles d’une matrice de score et d’une expression régulière. Application à la recherche de sites de fixation du facteur de transcription LXR. JOBIM 2015- 16e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. ⟨hal-01197050⟩

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