CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

Sonika Tyagi, Candida Vaz, Vipin Gupta, Rohit Bhatia, Sachin Maheshwari, Ashwin Srinivasan, Alok Bhattacharya

Research output: Contribution to journalArticleResearchpeer-review

37 Citations (Scopus)

Abstract

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at http://mirna.jnu.ac.in/cidmirna/.

Original languageEnglish
Pages (from-to)831-834
Number of pages4
JournalBiochemical and Biophysical Research Communications
Volume372
Issue number4
DOIs
Publication statusPublished - 8 Aug 2008

Keywords

  • microRNA
  • miRNA web server
  • RNA secondary structure
  • SCFG

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