Department of Mathematics and Statistics, University of Tromsø, 9037 Tromsø, Norway.
BMC Bioinformatics. 2010 Nov 23;11:573. doi: 10.1186/1471-2105-11-573.
Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox.
We present the DeltaProt Toolbox, a software toolbox that may be useful in importing, analyzing and visualizing data from multiple alignments of proteins. The toolbox has been written in MATLAB™ to provide an easy and user-friendly platform, including a graphical user interface, while ensuring good numerical performance. Problems in genome biology may be easily stated thanks to a compact input format. The toolbox also offers the possibility of utilizing structural information from the SABLE or other structure predictors. Different sequence plots can then be viewed and compared in order to find their similarities and differences. Detailed statistics are also calculated during the procedure.
The DeltaProt package is open source and freely available for academic, non-commercial use. The latest version of DeltaProt can be obtained from http://services.cbu.uib.no/software/deltaprot/. The website also contains documentation, and the toolbox comes with real data sets that are intended for training in applying the models to carry out bioinformatical and statistical analyses of protein sequences.Equipped with the new algorithms proposed here, DeltaProt serves as an auxiliary analysis tool capable of visualizing and comparing orthologus protein sequences. The framework of the algorithms also enables easy incorporation of extra information on structure, if such data is available.
统计生物信息学是通过适当的统计方法研究通过新技术获得的生物数据集。为了更好地理解蛋白质的环境适应性，可以探索和比较来自不同生境的同源序列。DeltaProt 工具包的主要目标是为用户提供比较筛选和极端蛋白及蛋白类研究所需的重要功能。数据集的可视化也是本文的重点，因为可视化可以在使各种关系透明方面发挥关键作用。本文旨在向读者介绍该工具包的存在、功能和适用性。
我们介绍了 DeltaProt 工具包，这是一个软件工具包，可用于导入、分析和可视化来自蛋白质多重比对的数据。该工具包是用 MATLAB™编写的，提供了一个易于使用的用户友好平台，包括图形用户界面，同时确保了良好的数值性能。由于紧凑的输入格式，可以轻松地提出基因组生物学问题。该工具包还提供了利用 SABLE 或其他结构预测器的结构信息的可能性。然后可以查看和比较不同的序列图，以找到它们的相似之处和不同之处。在过程中还计算了详细的统计信息。
DeltaProt 包是开源的，可供学术、非商业使用。最新版本的 DeltaProt 可从 http://services.cbu.uib.no/software/deltaprot/ 获得。该网站还包含文档，工具包附带了真实的数据集，旨在用于培训应用模型对蛋白质序列进行生物信息学和统计分析。配备了这里提出的新算法，DeltaProt 可以作为一种辅助分析工具，用于可视化和比较同源蛋白序列。如果有结构等额外信息，算法框架还可以方便地纳入这些信息。
