Laboratorio de Bioinformática Molecular, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
Bioinformatics. 2010 Jul 1;26(13):1664-5. doi: 10.1093/bioinformatics/btq252. Epub 2010 May 14.
Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications.
The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.
All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.
动态规划（DP）是一种通用的优化策略，在科学的各个领域都得到了成功的应用。在生物信息学中，它被广泛应用于计算蛋白质或 DNA 序列对之间的最佳比对。这些比对构成了新的、可验证的生物学假设的基础。尽管它很重要，但目前还没有用于培训和教育理解 DP 算法的交互式工具。在这里，我们引入了一个具有图形界面的交互式计算机应用程序，用于教育学生了解 DP。该程序显示 DP 评分矩阵和生成的最佳比对（多个），同时允许用户修改关键参数，如相似度矩阵中的值、序列比对算法版本以及缺口开放/延伸罚分。我们希望这个软件对生物信息学课程的教师和学生以及为各种应用实现 DP 算法的研究人员都有用。
该软件可免费在以下网址获得：http:/melolab.org/sat。该软件是用 Java 计算机语言编写的，因此可以在所有主要的平台和操作系统上运行，包括 Windows、Mac OS X 和 LINUX。
有关此软件的所有查询或意见都应发送至 Francisco Melo，电子邮件地址为 fmelo@bio.puc.cl。
