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Genomics Inform > Volume 9(1); 2011 > Article
MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics.
Dhandapani Vignesh, Paul Parameswari, Su Bin Im, Hae Jin Kim, Yong Pyo Lim
1Molecular Genetics and Genomics Laboratory, College of Agriculture and Life sciences, Chungnam National University, Daejeon 305-764, Korea. yplim@cnu.ac.kr
2Ensoltek Co., LTD, Daejeon 305-510, Korea.
Abstract
MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.
Keywords: miRNA; portable software; MiRPI; miRNA targets
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