Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China.
Bioinformatics. 2010 Feb 1;26(3):405-7. doi: 10.1093/bioinformatics/btp681. Epub 2009 Dec 10.
Motif discovery is an important topic in computational transcriptional regulation studies. In the past decade, many researchers have contributed to the field and many de novo motif-finding tools have been developed, each may have a different strength. However, most of these tools do not have a user-friendly interface and their results are not easily comparable. We present a software called Toolbox of Motif Discovery (Tmod) for Windows operating systems. The current version of Tmod integrates 12 widely used motif discovery programs: MDscan, BioProspector, AlignACE, Gibbs Motif Sampler, MEME, CONSENSUS, MotifRegressor, GLAM, MotifSampler, SeSiMCMC, Weeder and YMF. Tmod provides a unified interface to ease the use of these programs and help users to understand the tuning parameters. It allows plug-in motif-finding programs to run either separately or in a batch mode with predetermined parameters, and provides a summary comprising of outputs from multiple programs. Tmod is developed in C++ with the support of Microsoft Foundation Classes and Cygwin. Tmod can also be easily expanded to include future algorithms.
Tmod is available for download at http://www.fas.harvard.edu/~junliu/Tmod/.
基序发现是计算转录调控研究中的一个重要课题。在过去的十年中，许多研究人员对该领域做出了贡献，并开发了许多从头发现基序的工具，每个工具可能都有不同的优势。然而，这些工具大多没有用户友好的界面，其结果也不容易比较。我们为 Windows 操作系统开发了一个名为基序发现工具箱（Tmod）的软件。Tmod 的当前版本集成了 12 种广泛使用的基序发现程序：MDscan、BioProspector、AlignACE、Gibbs 基序采样器、MEME、CONSENSUS、MotifRegressor、GLAM、MotifSampler、SeSiMCMC、Weeder 和 YMF。Tmod 提供了一个统一的界面，方便用户使用这些程序，并帮助他们理解调整参数。它允许插件式基序发现程序单独运行或在预定参数的批处理模式下运行，并提供来自多个程序的输出摘要。Tmod 是用 C++编写的，支持 Microsoft 基础类和 Cygwin。Tmod 也可以很容易地扩展以包括未来的算法。
Tmod 可在 http://www.fas.harvard.edu/~junliu/Tmod/ 下载。
