Video Tip of the Week: MapMi, automated mapping of microRNA loci


Today’s video tip of the week is on MapMi. This tool is found at EBI and was developed by the Enright lab. The purpose of this tool is a computational system for mapping of miRNAs within and across species. As the abstract of their recent paper says:

 Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci… 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.

In today’s tip I walk you through MapMi to search for miRNAs.

ResearchBlogging.org

Quick link to MapMi: http://www.ebi.ac.uk/enright-srv/MapMi

Related Links:

miRBase (uses miRBase ID’s, our tutorial on miRBase here)
Ensembl  (uses Ensembl genomes, our tutorial on Ensembl here)
MapMi uses the next two algorithms for predictions:
RNAFold
Bowtie

Reference:

Guerra-Assuncao, J., & Enright, A. (2010). MapMi: automated mapping of microRNA loci BMC Bioinformatics, 11 (1) DOI: 10.1186/1471-2105-11-133