Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
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Pse-in-One：一个用于生成DNA、RNA和蛋白质序列多种伪组分模式的网络服务器。
DOI：
10.1093/nar/gkv458
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发表时间：
2015-07-01
影响因子：
14.9
通讯作者：
Chou KC
中科院分区：
文献类型：
--
作者：
Liu B;Liu F;Wang X;Chen J;Fang L;Chou KC
随着后基因组时代生物序列的大量产生，如何有效地表达生物样品（如DNA、RNA或蛋白质）的序列是计算生物学中最具挑战性的问题之一。虽然开发了几个Web服务器和独立工具来解决这个问题，但是所有这些工具只能处理一种类型的样本。此外，它们的内置属性的数量是有限的，因此用户通常难以根据其期望的特征或属性来配制生物序列。在本文中，由于内置属性数量多得多，我们将提出一种更灵活的Web服务器，称为Pse-in-One（http：//bioinformatics.hitsz.edu.cn/Pse-in-One/），它可以通过其28种不同的模式，生成DNA、RNA和蛋白质序列的几乎所有可能的特征向量。特别地，它还可以生成具有用户自己定义的属性的特征向量。这些特征向量可以很容易地与机器学习算法相结合，为生物信息学和系统生物学中的各种任务开发计算预测器和分析方法。可以预见，Pse-in-One Web服务器将成为计算蛋白质组学、基因组学以及生物序列分析中非常有用的工具。此外，为了最大限度地方便用户，其单机版也可以从http：//bioinformatics.hitsz.edu.cn/Pse-in-One/download/下载，并直接在Windows、Linux、Unix和Mac OS上运行。
With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems in computational biology is how to effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with a discrete model or a vector that can effectively reflect its sequence pattern information or capture its key features concerned. Although several web servers and stand-alone tools were developed to address this problem, all these tools, however, can only handle one type of samples. Furthermore, the number of their built-in properties is limited, and hence it is often difficult for users to formulate the biological sequences according to their desired features or properties. In this article, with a much larger number of built-in properties, we are to propose a much more flexible web server called Pse-in-One (http://bioinformatics.hitsz.edu.cn/Pse-in-One/), which can, through its 28 different modes, generate nearly all the possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature vectors with the properties defined by users themselves. These feature vectors can be easily combined with machine-learning algorithms to develop computational predictors and analysis methods for various tasks in bioinformatics and system biology. It is anticipated that the Pse-in-One web server will become a very useful tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users’ convenience, its stand-alone version can also be downloaded from http://bioinformatics.hitsz.edu.cn/Pse-in-One/download/, and directly run on Windows, Linux, Unix and Mac OS.
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