接近最优序列比对的可视化。
Visualization of near-optimal sequence alignments.
作者信息
Smoot Michael E, Guerlain Stephanie A, Pearson William R
机构信息
Department of Systems and Information Engineering, University of Virginia, Charlottesville, VA 22908, USA.
出版信息
Bioinformatics. 2004 Apr 12;20(6):953-8. doi: 10.1093/bioinformatics/bth013. Epub 2004 Jan 29.
MOTIVATION
Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.
RESULTS
We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.
动机
数学上最优的比对并不总是能正确地比对活性位点残基或公认的结构元件。大多数接近最优的序列比对算法显示的是替代比对路径，而非传统的逐个残基的两两比对。通常，这些方法没有提供在潜在的大量选项中有效找到最具生物学意义的比对的机制。
结果
我们开发了基于网络的软件，该软件将两个蛋白质或DNA序列的接近最优或替代比对显示为连续动画。一个到C++程序的万维网接口生成接近最优的比对，这些比对被发送到一个Java小程序，该小程序在一系列比对框架中显示它们。该小程序对残基进行比对，以便持续比对的区域在显示上保持固定位置，而可变区域则移动。可以停止显示以检查比对细节。
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