title: Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.
abstract: The microRNA (miRNA), a small non-coding RNA molecule, plays an important role in transcriptional and post-transcriptional regulation of gene expression. Its abnormal expression, however, has been observed in many cancers and other disease states, implying that the miRNA molecules are also deeply involved in these diseases, particularly in carcinogenesis. Therefore, it is important for both basic research and miRNA-based therapy to discriminate the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops). Most existing methods in this regard were based on the strategy in which RNA samples were formulated by a vector formed by their Kmer components. But the length of Kmers must be very short; otherwise, the vector's dimension would be extremely large, leading to the "high-dimension disaster" or overfitting problem. Inspired by the concept of "degenerate energy levels" in quantum mechanics, we introduced the "degenerate Kmer" (deKmer) to represent RNA samples. By doing so, not only we can accommodate long-range coupling effects but also we can avoid the high-dimension problem. Rigorous jackknife tests and cross-species experiments indicated that our approach is very promising. It has not escaped our notice that the deKmer approach can also be applied to many other areas of computational biology. A user-friendly web-server for the new predictor has been established at http://bioinformatics.hitsz.edu.cn/miRNA-deKmer/, by which users can easily get their desired results.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Gordon Life Science Institute, Boston, MA 0478, USA. Electronic address: bliu@insun.hit.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China. Electronic address: dragoncloudest@gmail.com.
authors.forename: Longyun
authors.initials: L
authors.lastname: Fang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China. Electronic address: wangshanyiwsy@gmail.com.
authors.forename: Shanyi
authors.initials: S
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China. Electronic address: wangxl@insun.hit.edu.cn.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Wendeng Marine Environmental Monitoring Station, Station Oceanic Administration Wendeng, Weihai, Shandong, China. Electronic address: lht760@126.com.
authors.forename: Hongtao
authors.initials: H
authors.lastname: Li
authors.affiliation: Gordon Life Science Institute, Boston, MA 0478, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: kcchou@gordonlifescience.org.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005822:Genetic Vectors / Q000235:genetics; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics*; D012322:RNA Precursors / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors
keywords: Degenerate Kmer; False pre-miRNA; Long-range effect; MicroRNA precursor; True pre-miRNA; deKmer web-server