BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
复制标题
DOI：
10.1002/prot.20527
复制
发表时间：
2005-10-01
影响因子：
2.9
通讯作者：
Poch, O
中科院分区：
文献类型：
--
作者：
Thompson, JD;Koehl, P;Poch, O
多序列比对是现代分子生物学的基石之一。它被用于鉴定保守基序，确定蛋白质结构域，通过同源性进行2D/3D结构预测和进化研究。最近，高通量技术，如基因组测序和结构蛋白质组学，导致爆炸的数量的序列和结构信息。作为响应，已经开发了几种新的多重比对方法，其提高了蛋白质比对的效率和质量。因此，用于评估和比较这些方法的基准也必须发展。我们在这里介绍最广泛使用的多重比对基准BAliBASE的最新版本，它提供了基于3D结构叠加的高质量、手动细化的参考比对。BAliBASE 3.0版包括新的、更具挑战性的测试用例，代表了在比对大型复杂序列集时遇到的真实的问题。使用一种新的，半自动的更新协议，在基准的蛋白质家族的数量已经增加，现在有代表性的测试案例，涵盖了大部分的蛋白质折叠空间。BAliBASE中的蛋白质总数也从1444个序列显著增加到6255个序列。此外，现在为所有测试案例提供全长序列，这代表了全局和局部比对程序的困难案例。最后，BAliBASE网站（http：//www-bio3d-igbmc.ustrasbg.frfbalibase）已经完全重新设计，为BAliBASE参考比对和相关注释的可视化提供更加用户友好的交互式界面。
Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site (http://www-bio3d-igbmc.ustrasbg.frfbalibase) has been completely redesigned to provide a more user-friendly, interactive interface for the visualization of the BAliBASE reference alignments and the associated annotations.