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GECKO is a genetic algorithm to classify and explore high throughput sequencing data

Thomas Aubin, Barriere sylvain, Broseus Lucile, Brooke Julie, Lorenzi Claudio, Villemin Jean-Philippe, Beurier Grégory, Sabatier Robert, Reynes Christelle, Mancheron Alban, Ritchie William. 2019. GECKO is a genetic algorithm to classify and explore high throughput sequencing data. Communications Biology, 2:222, 8 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : BIOLOGY

Abstract : Comparative analysis of high throughput sequencing data between multiple conditions often involves mapping of sequencing reads to a reference and downstream bioinformatics analyses. Both of these steps may introduce heavy bias and potential data loss. This is especially true in studies where patient transcriptomes or genomes may vary from their references, such as in cancer. Here we describe a novel approach and associated software that makes use of advances in genetic algorithms and feature selection to comprehensively explore massive volumes of sequencing data to classify and discover new sequences of interest without a mapping step and without intensive use of specialized bioinformatics pipelines. We demonstrate that our approach called GECKO for GEnetic Classification using k-mer Optimization is effective at classifying and extracting meaningful sequences from multiple types of sequencing approaches including mRNA, microRNA, and DNA methylome data.

Mots-clés Agrovoc : Bioinformatique, Sciences médicales, Séquence d'ADN, apprentissage machine

Mots-clés complémentaires : Algorithme, Algorithme génétique, machine learning

Mots-clés libres : Genetic Algorithm, High throughput sequencing, Machine learning, Predictive medecine

Classification Agris : U10 - Computer science, mathematics and statistics
000 - Other themes

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Thomas Aubin, CNRS (FRA)
  • Barriere sylvain, CNRS (FRA)
  • Broseus Lucile, CNRS (FRA)
  • Brooke Julie, CNRS (FRA)
  • Lorenzi Claudio, CNRS (FRA)
  • Villemin Jean-Philippe, CNRS (FRA)
  • Beurier Grégory, CIRAD-BIOS-UMR AGAP (FRA)
  • Sabatier Robert, UM1 (FRA)
  • Reynes Christelle, UM1 (FRA)
  • Mancheron Alban, CNRS (FRA)
  • Ritchie William, CNRS (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/592942/)

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