APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
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DOI：
10.1093/bioinformatics/btg1029
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发表时间：
2003-07-01
期刊：
影响因子：
5.8
通讯作者：
Notredame, Cedric
中科院分区：
文献类型：
--
作者：
O'Sullivan, Orla;Zehnder, Mark;Notredame, Cedric
动机：我们描述了APDB，一种新的评估蛋白质序列比对质量的指标，给定两个或更多的PDB结构。这种评估不需要参考对齐或结构叠加。结果：使用已有的参考多序列比对集合和已有的比对方法，APDB给出的结果与传统评价得到的结果是一致的。我们还表明，APDB适合于评估结构相同的序列比对。我们的结论是，APDB提供了一种替代更传统的方法来对序列比对包进行基准测试的方法。
Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods.Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.