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Int. J. Mol. Sci. 2017, 18(11), 2400; doi:10.3390/ijms18112400

UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences

1
School of Computer Science and Technology, Tianjin University, Tianjin 300350, China
2
School of Chemical Engineering, Tianjin University, Tianjin 300350, China
3
Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
*
Author to whom correspondence should be addressed.
Received: 10 October 2017 / Revised: 1 November 2017 / Accepted: 3 November 2017 / Published: 14 November 2017
(This article belongs to the Special Issue Special Protein Molecules Computational Identification)
View Full-Text   |   Download PDF [1487 KB, uploaded 14 November 2017]   |  

Abstract

With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository. View Full-Text
Keywords: pseudo-amino acid compositions; pseudo-k nucleotide compositions; extensible software pseudo-amino acid compositions; pseudo-k nucleotide compositions; extensible software
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Du, P.-F.; Zhao, W.; Miao, Y.-Y.; Wei, L.-Y.; Wang, L. UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences. Int. J. Mol. Sci. 2017, 18, 2400.

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