De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures

作者: Kwang Loong Stanley Ng , Santosh K. Mishra

DOI: 10.1093/BIOINFORMATICS/BTM026

关键词: Phylogenetic treeComputational biologySimilarity measureGeneticsSupplementary dataSupport vector machineGeneGaussian radial basis functionmicroRNAInverted repeatBiology

摘要: … the miRNAs biogenesis, the hairpin structure is a necessary feature for the computational classification of novel precursor miRNAs … species-specific pre-miRs are likely to remain elusive. …

参考文章(72)
Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Gan, Tamar Schlick, RAG: RNA-As-Graphs web resource BMC Bioinformatics. ,vol. 5, pp. 88- 88 ,(2004) , 10.1186/1471-2105-5-88
Eva Freyhult, Paul P Gardner, Vincent Moulton, A comparison of RNA folding measures BMC Bioinformatics. ,vol. 6, pp. 241- 241 ,(2005) , 10.1186/1471-2105-6-241
Gary Ruvkun, Brenda J. Reinhart, Frank J. Slack, Michael Basson, Amy E. Pasquinelli, Jill C. Bettinger, Ann E. Rougvie, H. Robert Horvitz, The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature. ,vol. 403, pp. 901- 906 ,(2000) , 10.1038/35002607
Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang, Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine BMC Bioinformatics. ,vol. 6, pp. 310- 310 ,(2005) , 10.1186/1471-2105-6-310
Amy E Pasquinelli, Brenda J Reinhart, Frank Slack, Mark Q Martindale, Mitzi I Kuroda, Betsy Maller, David C Hayward, Eldon E Ball, Bernard Degnan, Peter Müller, Jürg Spring, Ashok Srinivasan, Mark Fishman, John Finnerty, Joseph Corbo, Michael Levine, Patrick Leahy, Eric Davidson, Gary Ruvkun, None, Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA Nature. ,vol. 408, pp. 86- 89 ,(2000) , 10.1038/35040556
Peter Sarnow, Catherine L. Jopling, Kara L. Norman, Sylvia Schütz, Karen A. Wehner, MicroRNAs: expression, avoidance and subversion by vertebrate viruses. Nature Reviews Microbiology. ,vol. 4, pp. 651- 659 ,(2006) , 10.1038/NRMICRO1473
Lee P Lim, Margaret E Glasner, Soraya Yekta, Christopher B Burge, David P Bartel, Vertebrate microRNA genes. Science. ,vol. 299, pp. 1540- 1540 ,(2003) , 10.1126/SCIENCE.1080372
R. C. Lee, An Extensive Class of Small RNAs in Caenorhabditis elegans Science. ,vol. 294, pp. 862- 864 ,(2001) , 10.1126/SCIENCE.1065329
Jinfeng Liu, Julian Gough, Burkhard Rost, PLoS Genetics EIC Wayne Frankel, Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines PLOS Genetics. ,vol. 2, ,(2006) , 10.1371/JOURNAL.PGEN.0020029