PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
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DOI：
10.1016/j.ab.2014.04.001
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发表时间：
2014-07-01
影响因子：
2.9
通讯作者：
Chou, Kuo-Chen
中科院分区：
文献类型：
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作者：
Chen, Wei;Lei, Tian-Yu;Chou, Kuo-Chen
伪寡核苷酸组成，或伪K-字节组核苷酸组成(PseKNC)，可以用离散的模型或载体来表示DNA或RNA序列，但仍然通过其组成的寡核苷酸的物理化学性质保持相当大的序列顺序信息，特别是全局或远程序列顺序信息。因此，PseKNC方法在处理计算基因组学和基因组序列分析中的许多问题方面具有很高的潜力。然而，处理不同的DNA或RNA问题可能需要不同类型的PseKNC。在这里，我们提出了一个灵活和用户友好的PseKNC(在http://lin.uestc.edu.cn/pseknc/default.aspx))的Web服务器，用户可以通过选择各种参数和物理化学性质，根据自己的需要轻松地生成多种不同模式的PseKNC。此外，为了方便大多数实验科学家，还提供了一个逐步指南，指导如何使用现有的Web服务器来生成他们想要的PseKNC，而不需要遵循本文中提出的复杂的数学方程，这些方程只是为了完整地描述PseKNC及其发展而提出的。预计PseKNC网络服务器将成为计算基因组学和基因组序列分析中非常有用的工具。(C)2014 Elsevier Inc.保留所有权利。
The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. (C) 2014 Elsevier Inc. All rights reserved.