Searching the coding region for microRNA targets

  1. Jiří Vaníček3
  1. Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
    1. 1 These authors contributed equally to this work.

    • 2 Present address: Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland

    Abstract

    Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for conserved motifs that are complementary to the microRNA seed region and also overrepresented in comparison with a background model preserving both codon usage and amino acid sequence. Precision and sensitivity of PACCMIT-CDS are evaluated using PAR-CLIP and proteomics data sets. Thanks to the properly constructed background, the new algorithm achieves a lower rate of false positives and better ranking of predictions than do currently available algorithms, which were designed to find microRNA targets within 3′ UTRs.

    Keywords

    Footnotes

    • 3 Corresponding author

      E-mail jiri.vanicek{at}epfl.ch

    • Received July 21, 2012.
    • Accepted December 1, 2012.

    Freely available online through the RNA Open Access option.

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