Structural Chemistry Program, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Qld 4111, Australia.
Bioinformatics. 2012 Apr 1;28(7):1026-7. doi: 10.1093/bioinformatics/bts035. Epub 2012 Feb 12.
Both alignment generation and visualization are important processes for producing biologically meaningful sequence alignments. Computational tools that combine reliable, automated and semi-automated approaches to produce secondary structure-based alignments with an appropriate visualization of the results are rare. We have developed SBAL, a tool to generate and edit secondary structure-based sequence alignments. It is easy to install and provides a user-friendly interface. Sequence alignments are displayed, with secondary structure assignments mapped to their corresponding regions in the sequence by using a simple colour scheme. The algorithm implemented for automated and semi-automated secondary structure-based alignment calculations shows a comparable performance to existing software.
SBAL has been implemented in Java to provide cross-platform compatibility. SBAL is freely available to academic users at http://www.structuralchemistry.org/pcsb/. Users will be asked for their name, institution and email address. A manual can also be downloaded from this site. The software, manual and test sets are also available as supplementary material.
Supplementary data are available at Bioinformatics online.
对齐生成和可视化对于生成具有生物学意义的序列对齐都是重要的过程。将可靠的、自动化和半自动化方法结合起来，生成基于二级结构的对齐，并对结果进行适当的可视化的计算工具非常少见。我们开发了 SBAL，这是一种用于生成和编辑基于二级结构的序列对齐的工具。它易于安装，并提供了用户友好的界面。序列对齐以简单的颜色方案显示，将二级结构分配映射到序列中相应的区域。用于自动化和半自动基于二级结构的对齐计算的算法与现有软件的性能相当。
SBAL 已用 Java 实现，以提供跨平台兼容性。SBAL 可在学术用户免费使用，网址为 http://www.structuralchemistry.org/pcsb/。用户将被要求提供他们的姓名、机构和电子邮件地址。也可以从该网站下载手册。软件、手册和测试集也可作为补充材料获得。
补充数据可在 Bioinformatics 在线获得。
