Genomics & Informatics

  • 제9권1호
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  • Pages.39-43
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  • 2011
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  • 1598-866X(pISSN)
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  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
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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)
  • 심사 : 2011.03.10
  • 발행 : 2011.03.31
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초록

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.

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참고문헌

  1. Ambros, V. (2004). The functions of animal microRNAs. Nature 431, 350-355. https://doi.org/10.1038/nature02871
  2. Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297. https://doi.org/10.1016/S0092-8674(04)00045-5
  3. Bartel, D.P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233. https://doi.org/10.1016/j.cell.2009.01.002
  4. Elbashir, S.M., Lendeckel. W., and Tuschl, T. (2001). RNA interference is mediated by 21 and 22 nt RNAs. Genes & Development. 15, 188-200. https://doi.org/10.1101/gad.862301
  5. Kim, V.N. (2005). MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6, 376-385.
  6. 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. https://doi.org/10.1016/0092-8674(93)90529-Y
  7. Lim, L.P., Lau, N.C., and Weinstein, E.G. (2003). The microRNAs of Caenorhabditis elegans. Genes & Development 17, 991-1008. https://doi.org/10.1101/gad.1074403
  8. 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. https://doi.org/10.1016/S0092-8674(02)00863-2
  9. Quintana, M.L., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science 294, 853-858. https://doi.org/10.1126/science.1064921
  10. 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. https://doi.org/10.1016/S0092-8674(02)00863-2
  11. 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. https://doi.org/10.1101/gr.2722704
  12. Ruvkun, G. (2001). Molecular Biology: Glimpses of a Tiny RNA World. Science 294, 797-799. https://doi.org/10.1126/science.1066315
  13. Zhang, B., Stellwag, E.J., and Pan, X. (2009). Large-scale genome analysis reveals unique features of miRNAs. Gene. 443, 100-109. https://doi.org/10.1016/j.gene.2009.04.027
  14. 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. https://doi.org/10.1093/nar/gkp818

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