IMR Press / FBL / Volume 19 / Issue 3 / DOI: 10.2741/4221

Frontiers in Bioscience-Landmark (FBL) is published by IMR Press from Volume 26 Issue 5 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Article

Identification of C. elegans & C. briggsae miRNAs by modified miRsearch

Show Less
1 Molecular and Human Genetics Division, Indian Institute of Chemical Biology, Kolkata-700032, India
2 National Cancer Institute, NIH, Building 37 room 3128, Bethesda, MD 20892, USA
3 Human Genetics Unit, Biological Science Division, ISI, 700108, Kolkata
Academic Editor:Raghunath Chatterjee
Front. Biosci. (Landmark Ed) 2014, 19(3), 504–514; https://doi.org/10.2741/4221
Published: 1 January 2014
(This article belongs to the Special Issue Epigenetics, non-coding RNAs and gene regulation)
Abstract

In this study, a modified miRsearch program was developed in C++ for the detection of miRNAs. All the mature miRNA sequences of Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remanei, Drosophila melanogaster, Homo sapiens and Rattus norvegicus available in miRbase was searched by this program for homologous sequences with a maximum of 3-mismatches in the chromosomes of C. elegans excluding the miRNAs of C. elegans. The same strategy was repeated for C. briggsae excluding C. briggsae miRNAs. The probable pre-miRNA sequences with stem loop secondary structures were assessed by implementation of longest-common-subsequence (LCS) algorithm with appropriate scoring system. As miRNA genes could be on either strand, each sequence was searched in both forward and reverse strands. The putative miRNAs were viewed through Mapviewer to identify their intronic or intergenic location in C. elegans and C. briggsae genomes. Further, the quality of stem-loop formation of the remaining pre-miRNA sequences was assessed through RNAFOLD. This algorithm will be helpful in detection of potential miRNAs in future sequencing data, making this an invaluable tool for miRNA prediction.

Keywords
miRNA
C. elegans and C. briggasae miRNA
Modified Mirsearch
Share
Back to top