title: Searching the coding region for microRNA targets.
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.
authors: École Polytechnique Fédérale de Lausanne,CH-1015 Lausanne, Switzerland.
authors: Ray M
authors: RM
authors: Marín
authors: Miroslav
authors: M
authors: Sulc
authors: Jirí
authors: J
authors: Vanícek
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D003062:Codon; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D012680:Sensitivity and Specificity
chemical_list: D020413:3' Untranslated Regions; D003062:Codon; D035683:MicroRNAs
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