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repRNA: a web server for generating various feature vectors of RNA sequences

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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/.

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Acknowledgments

The authors wish to thank the three anonymous reviewers for the constructive comments, which were very useful to strengthening the presentation of this paper.

Conflict of interest

The authors declare no competing interests.

Funding

This work was supported by the National Natural Science Foundation of China (61300112 and 61272383), the Scientific Research Innovation Foundation in Harbin Institute of Technology (Project No. HIT.NSRIF.2013103), the Project Sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and Shenzhen Municipal Science and Technology Innovation Council (Grant No. CXZZ20140904154910774), and National High Technology Research and Development Program of China (863 Program) [2015AA015405].

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Authors and Affiliations

  1. School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China

    Bin Liu, Fule Liu, Longyun Fang & Xiaolong Wang

  2. Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, 518055, Guangdong, China

    Bin Liu & Xiaolong Wang

  3. Gordon Life Science Institute, Boston, MA, 02478, USA

    Bin Liu & Kuo-Chen Chou

  4. Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia

    Kuo-Chen Chou

Authors
  1. Bin Liu
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  2. Fule Liu
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  3. Longyun Fang
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  4. Xiaolong Wang
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  5. Kuo-Chen Chou
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Correspondence to Bin Liu.

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Communicated by S. Hohmann.

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Liu, B., Liu, F., Fang, L. et al. repRNA: a web server for generating various feature vectors of RNA sequences. Mol Genet Genomics 291, 473–481 (2016). https://doi.org/10.1007/s00438-015-1078-7

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