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Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(7):841-845; doi:10.1093/bioinformatics/bti073
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Profile-based detection of microRNA precursors in animal genomes

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

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

*To whom correspondence should be addressed.

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.

Contact: gautheret{at}esil.univ-mrs.fr


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