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MapMi: automated mapping of microRNA loci

José Afonso Guerra-Assunção12 and Anton J Enright1*

Author affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

2 PDBC, Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal

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Citation and License

BMC Bioinformatics 2010, 11:133  doi:10.1186/1471-2105-11-133

Published: 16 March 2010

Abstract

Background

A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. However, miRBase focuses on those species for which miRNAs have been directly confirmed. Secondly, specific miRNAs or their loci are sometimes not annotated even in well-covered species. We sought to address this problem by developing a computational system for automated mapping of miRNAs within and across species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. Our primary goal is not the discovery of novel miRNAs but the mapping of validated miRNAs in one species to their most likely orthologues in other species.

Results

We present MapMi, a computational system for automated miRNA mapping across and within species. This method has a sensitivity of 92.20% and a specificity of 97.73%. Using the latest release (v14) of miRBase, we obtained 10,944 unannotated potential miRNAs when MapMi was applied to all 21 species in Ensembl Metazoa release 2 and 46 species from Ensembl release 55.

Conclusions

The pipeline and an associated web-server for mapping miRNAs are freely available on http://www.ebi.ac.uk/enright-srv/MapMi/ webcite. In addition precomputed miRNA mappings of miRBase miRNAs across a large number of species are provided.