title: LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.
abstract: Supervised classification based on support vector machines (SVMs) has successfully been used for the prediction of cis-regulatory modules (CRMs). However, no integrated tool using such heterogeneous data as position-specific scoring matrices, ChIP-seq data or conservation scores is currently available. Here, we present LedPred, a flexible SVM workflow that predicts new regulatory sequences based on the annotation of known CRMs, which are associated to a large variety of feature types. LedPred is provided as an R/Bioconductor package connected to an online server to avoid installation of non-R software. Due to the heterogeneous CRM feature integration, LedPred excels at the prediction of regulatory sequences in Drosophila and mouse datasets compared with similar SVM-based software.
  
  
  
  LedPred is available on GitHub: https://github.com/aitgon/LedPred and Bioconductor: http://bioconductor.org/packages/release/bioc/html/LedPred.html under the MIT license.
  
  
  
  aitor.gonzalez@univ-amu.fr
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France.
authors.forename: Denis
authors.initials: D
authors.lastname: Seyres
authors.affiliation: Cancer Research UK, London Research Institute, London WC2A 3LY, UK.
authors.forename: Elodie
authors.initials: E
authors.lastname: Darbo
authors.affiliation: INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France, CNRS, Marseille, France and.
authors.forename: Laurent
authors.initials: L
authors.lastname: Perrin
authors.affiliation: IPMB, Universität Heidelberg and Department of Theoretical Bioinformatics, DKFZ, Heidelberg 69120, Germany.
authors.forename: Carl
authors.initials: C
authors.lastname: Herrmann
authors.affiliation: INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France.
authors.forename: Aitor
authors.initials: A
authors.lastname: González
mesh_terms: D000818:Animals; D003196:Computer Graphics; D004330:Drosophila; D005786:Gene Expression Regulation; D053858:Metabolic Networks and Pathways; D051379:Mice; D058977:Molecular Sequence Annotation; D012984:Software; D060388:Support Vector Machine; D018511:Systems Integration