Efficient algorithms for the identification of miRNA motifs in DNA sequences
Nuno D. Mendes,
INESC-ID Lisboa and IST –
Abstract:
In the last decade, a novel gene expression regulatory mechanism was discovered. It is mediated by RNA molecules named miRNAs and it acts by silencing target genes. Despite the advancements in this research field, we are still not able to rigourously characterise miRNA genes in order to identify the sequence, structure or contextual requirements that are needed to obtain a functional miRNA.
In this work we present a strategy to sieve through the vast amount of stem-loops that can be found in metazoan genomes, significantly reducing the set of candidates while retaining most known miRNA precursors. The approach relies on a combination of robustness measures, on the analysis of precursor structure, and on the incorporation of information about the transcription potential of each candidate.
The methodology was applied to the genomes of Drosophila melanogaster and Anopheles gambiae, and to homologs of known precursors in the newly sequenced Anopheles darlingi. We obtain, thus, a restricted and ordered set of candidates for these organisms which fulfil the established prerequisites.
Keywords: miRNA, gene finding, single-genome, robustness, stability, secondary structure
Date: 2011-Apr-01 Time: 14:00:00 Room: 020
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