miRNAminer: a tool for homologous microRNA gene search

BMC Bioinformatics. 2008 Jan 23;9:39. doi: 10.1186/1471-2105-9-39.

Abstract

Background: MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental and computational methods were used to construct miRNA gene repositories agreeing with careful submission guidelines.

Results: An algorithm we developed - miRNAminer - is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to asses their fidelity. When applying miRNAminer on seven mammalian species we identified several hundreds of high-confidence homologous miRNAs increasing the total collection of (miRbase) miRNAs, in these species, by more than 50%. miRNAminer uses stringent criteria and exhibits high sensitivity and specificity.

Conclusion: We present - miRNAminer - the first web-server for homologous miRNA gene search in animals. miRNAminer can be used to identify conserved homolog miRNA genes and can also be used prior to depositing miRNAs in public databases. miRNAminer is available at http://pag.csail.mit.edu/mirnaminer.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Base Sequence
  • Cattle
  • Databases, Genetic / trends
  • Dogs
  • Humans
  • Internet / trends
  • Mice
  • MicroRNAs / analysis
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Opossums
  • Pan troglodytes
  • Rats
  • Sequence Homology, Nucleic Acid*

Substances

  • MicroRNAs