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.
展开▼
机译：动机：数学上最佳的比对方法并不总是总是正确地比对活性位点残基或公认的结构元素。大多数接近最佳的序列比对算法显示替代的比对路径，而不是常规的逐残基成对比对。通常，这些方法不提供在潜在的大量选项中有效找到最具有生物学意义的比对的机制。结果：我们开发了基于Web的软件，该软件可以将两个蛋白质或DNA序列的接近或最佳比对显示为连续的动态图像。 C ++程序的WWW接口生成接近最佳的对齐方式，该对齐方式被发送到Java Applet，后者以一系列对齐方式显示它们。小程序对齐残基，以便一致对齐的区域保留在显示器上的固定位置，而可变区域则移动。可以停止显示以检查对齐详细信息。
展开▼
