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http://dx.doi.org/10.5808/GI.2011.9.1.039

MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics  

Vignesh, Dhandapani (Molecular Genetics and Genomics Laboratory, College of Agriculture and Life sciences, Chungnam National University)
Parameswari, Paul (Molecular Genetics and Genomics Laboratory, College of Agriculture and Life sciences, Chungnam National University)
Im, Su-Bin (Molecular Genetics and Genomics Laboratory, College of Agriculture and Life sciences, Chungnam National University)
Kim, Hae-Jin (Ensoltek Co., LTD.)
Lim, Yong-Pyo (Molecular Genetics and Genomics Laboratory, College of Agriculture and Life sciences, Chungnam National University)
Publication Information
Genomics & Informatics / v.9, no.1, 2011 , pp. 39-43 More about this Journal
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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1 Lee, R.C., Feinbaum, R.L., and Ambros, V. (1993). The Caenorhabditis elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.   DOI
2 Lim, L.P., Lau, N.C., and Weinstein, E.G. (2003). The microRNAs of Caenorhabditis elegans. Genes & Development 17, 991-1008.   DOI
3 Lim, L.P., Matthew, W., Rhoades, M.W., Reinhart, B.J., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant MicroRNA targets. Cell 110, 513-520.   DOI
4 Quintana, M.L., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.   DOI   ScienceOn
5 Rhoades, M.W., Reinhart, B.J., Lim, L. P., Burge, C. B., Bartel, B., and Bartel, D. P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520.   DOI
6 Rodriguez, A., Jones, S.G., Ashurt, J.L., and Bradley, A. (2004). Identification of Mammalian microRNA Host Genes and Transcription Units. Genome Research 14, 1902-1910.   DOI
7 Ruvkun, G. (2001). Molecular Biology: Glimpses of a Tiny RNA World. Science 294, 797-799.   DOI
8 Zhang, B., Stellwag, E.J., and Pan, X. (2009). Large-scale genome analysis reveals unique features of miRNAs. Gene. 443, 100-109.   DOI
9 Zhang, Z., Yu, J., Li, D., Zhang, Z., Liu, F., Zhou, X., Wang, T., Ling, Yi., and Su, Z. (2010). PMRD: plant microRNA database. Nucl. Acids Res. 38(suppl 1), D806-813.   DOI   ScienceOn
10 Ambros, V. (2004). The functions of animal microRNAs. Nature 431, 350-355.   DOI
11 Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.   DOI
12 Bartel, D.P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.   DOI
13 Elbashir, S.M., Lendeckel. W., and Tuschl, T. (2001). RNA interference is mediated by 21 and 22 nt RNAs. Genes & Development. 15, 188-200.   DOI
14 Kim, V.N. (2005). MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6, 376-385.