Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.

Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3^′-untranslated regions (3^′-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3^′-UTR target sites. Further analysis indicates that genes with shorter 3^′-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3^′-UTR.

Availability: The results of DIANA-microT-CDS are available at www.microrna.gr/microT-CDS

Contact:  hatzigeorgiou@fleming.gr; reczko@fleming.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.