The sufficient minimal set of miRNA seed types.

ABSTRACT:

Motivation

Pairing between the target sequence and the 6-8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest.

Results

We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found t

SUBMITTER: Ellwanger DC 

PROVIDER: S-EPMC3087955 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature