LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines

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Seyres, Denis | Darbo, Elodie | Perrin, Laurent | Herrmann, Carl | Gonzalez, Aitor

Edité par CCSD ; Oxford University Press (OUP) -

International audience. 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.

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