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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti073
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 12, 2004
Revised September 17, 2004
Accepted September 18, 2004

Discovery note

Profile-based detection of microRNA precursors in animal genomes

Matthieu Legendre 1, André Lambert 2, and Daniel Gautheret 1*

1 INSERM ERM-206, Luminy Case 928, 13288 Marseille Cedex 09, France
2 CNRS UMR6207, Luminy case 907, 13288 Marseille Cedex 09, France

* To whom correspondence should be addressed.
Daniel Gautheret, E-mail: gautheret{at}tagc.univ-mrs.fr


  Abstract

Motivation: MicroRNAs (miRNA) are essential 21-22 nt regulatory RNAs produced from larger hairpin-like precursors. Local sequence alignment tools such as BLAST are able to identify new members of known miRNA families, but not all of them. We set out to estimate how many new miRNAs could be recovered using a profile-based strategy such as that implemented in the ERPIN program.

Results: We constructed alignments for 18 miRNA families and performed ERPIN searches on animal genomes. Results were compared to those of a WU-BLAST search at the same E-value cutoff. The two combined approaches produced 265 new miRNA candidates that were not found in miRNA databases. About 17% of hits were ERPIN-specific. They showed better structural characteristics than BLAST-specific hits and included interesting candidates such as members of the miR-17 cluster in Tetraodon. Profile-based RNA detection will be an important complement of similarity search programs in the completion of miRNA collections.


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