Artif Intell Med - PMirP: a pre-microRNA prediction method based on structure-sequence hybrid features.

Tópicos

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Resumo

JECTIVE: MicroRNA is a type of small non-coding RNAs, which usually has a stem-loop structure. As an important stage of microRNA, the pre-microRNA is transported from nuclear to cytoplasm by exportin5 and finally cleaved into mature microRNA. Structure-sequence features and minimum of free energy of secondary structure have been used for predicting pre-microRNA. Meanwhile, the double helix structure with free nucleotides and base-pairing features is used to identify pre-miRNA for the first time.METHODS: We applied support vector machine for a novel hybrid coding scheme using left-triplet method, the free nucleotides, the minimum of free energy of secondary structure and base-pairings features. Data sets of human pre-microRNA, other 11 species and the latest pre-microRNA sequences were used for testing.RESULTS: In this study we developed an improved method for pre-microRNA prediction using a combination of various features and a web server called PMirP. The prediction specificity and sensitivity for real and pseudo human pre-microRNAs are as high as 98.4% and 94.9%, respectively. The web server is freely available to the public at http://ccst.jlu.edu.cn/ci/bioinformatics/MiRNA (accessed: 26 February 2010).CONCLUSIONS: Experimental results show that the proposed method improves the prediction efficiency and accuracy over existing methods. In addition, the PMirP has lower computational complexity and higher throughput prediction capacity than Mipred web server.

Resumo Limpo

jectiv microrna type small noncod rnas usual stemloop structur import stage microrna premicrorna transport nuclear cytoplasm exportin final cleav matur microrna structuresequ featur minimum free energi secondari structur use predict premicrorna meanwhil doubl helix structur free nucleotid basepair featur use identifi premirna first timemethod appli support vector machin novel hybrid code scheme use lefttriplet method free nucleotid minimum free energi secondari structur basepair featur data set human premicrorna speci latest premicrorna sequenc use testingresult studi develop improv method premicrorna predict use combin various featur web server call pmirp predict specif sensit real pseudo human premicrorna high respect web server freeli avail public httpccstjlueducncibioinformaticsmirna access februari conclus experiment result show propos method improv predict effici accuraci exist method addit pmirp lower comput complex higher throughput predict capac mipr web server

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