BAliBASE

A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.

本数据集汇聚了高质量的多序列比对，旨在对比对算法进行客观、比较性研究。这些比对基于三维结构叠加构建，并经过人工精细调整以确保关键功能残基的对齐。数据集定义了多个子集，涵盖在比对真实蛋白质集合时遇到的大多数重要问题。该数据集特别设计为评估资源，旨在解决在比对完整序列时遇到的所有问题。首次发布提供了处理高变异性、不均匀分配以及大的N/C端延伸和内部插入问题的参考比对集。数据库的2.0版本整合了包含结构重复、跨膜序列和环形排列的三组新的参考比对集，以评估对这些复杂序列的检测/预测和对齐的准确性。在资源内部，用户可以查看所有比对的列表，通过ftp下载整个数据库，获取用于将测试比对与BAIbase参考比对进行比较的“c”程序（该程序源代码免费提供），或查看使用BAIbase参考比对集进行的多个比对程序比较研究的成果。

搜集汇总

背景与挑战

背景概述

BAliBASE是一个高质量的蛋白质多序列比对数据库，专门用于评估比对算法的性能。其特点包括基于3D结构叠加构建的比对、手动精修以确保功能残基对齐，并包含多种复杂序列问题的子集，如高变异性、跨膜序列和环形置换等。