Robust Tools for Biological Sequence Analysis

亚利桑那大学获得了一项拨款，用于开发一种计算机程序，使用一种新的、新颖的方法来比对蛋白质序列，特别是整个基因组的序列。该计划将专注于基因序列比对中最令人望而生畏的两个问题：非常具体地比对小范围的蛋白质序列，以及不太具体但非常有防御性的将许多序列比对在一起。该提议是开发一套强大的、集成的开源工具，使用在该领域新颖的计算机科学技术来进行本地和多个比对，并产生确保找到最佳解决方案的准确算法。所产生的算法将使用具有公布基准的真实数据和具有已知最佳比对的模拟数据进行仔细测试。

A grant has been awarded to the University of Arizona to develop a computer program to use a new and novel way of aligning protein sequences, especially those of whole genomes. The program will focus on two of the most daunting issues in aligning gene sequences: very specifically aligning small areas of protein sequences and less specifically but very defensibly aligning many sequences together. The proposal is to develop a robust and integrated suite of open-source tools to do both local and multiple alignments using a computer science technique that is novel in this arena and that yields exact algorithms guaranteed to find optimal solutions. The resulting algorithms will be carefully tested using both real data with published benchmarks and simulated data with known optimal alignments.