title: repRNA: a web server for generating various feature vectors of RNA sequences.
abstract: With the rapid growth of RNA sequences generated in the postgenomic age, it is highly desired to develop a flexible method that can generate various kinds of vectors to represent these sequences by focusing on their different features. This is because nearly all the existing machine-learning methods, such as SVM (support vector machine) and KNN (k-nearest neighbor), can only handle vectors but not sequences. To meet the increasing demands and speed up the genome analyses, we have developed a new web server, called "representations of RNA sequences" (repRNA). Compared with the existing methods, repRNA is much more comprehensive, flexible and powerful, as reflected by the following facts: (1) it can generate 11 different modes of feature vectors for users to choose according to their investigation purposes; (2) it allows users to select the features from 22 built-in physicochemical properties and even those defined by users' own; (3) the resultant feature vectors and the secondary structures of the corresponding RNA sequences can be visualized. The repRNA web server is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/repRNA/ .
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China. bliu@gordonlifescience.org.|Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China. bliu@gordonlifescience.org.|Gordon Life Science Institute, Boston, MA, 02478, USA. bliu@gordonlifescience.org.
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, 518055, Guangdong, China. liufule12@gmail.com.
authors.forename: Fule
authors.initials: F
authors.lastname: Liu
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China. 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, 518055, Guangdong, China. wangxl@insun.hit.edu.cn.|Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China. wangxl@insun.hit.edu.cn.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Gordon Life Science Institute, Boston, MA, 02478, USA. kcchou@gordonlifescience.org.|Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia. kcchou@gordonlifescience.org.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016678:Genome / Q000235:genetics; D020407:Internet; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: D012313:RNA
keywords: Physicochemical properties; PseAAC; PseKNC; Secondary structure of RNA; User-defined properties; repDNA; repRNA