  3' untranslated regions (3' UTRs) contain binding sites for many regulatory
elements, and in particular for microRNAs (miRNAs). The importance of
miRNA-mediated post-transcriptional regulation has become increasingly clear in
the last few years.
  We propose two complementary approaches to the statistical analysis of
oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of
candidate binding sites for regulatory elements. The first method is based on
the identification of sets of genes characterized by evolutionarily conserved
overrepresentation of an oligonucleotide. The second method is based on the
identification of oligonucleotides showing statistically significant strand
asymmetry in their distribution in 3' UTRs.
  Both methods are able to identify many previously known binding sites located
in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates
are proposed for experimental verification.
