Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
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DOI：
10.1016/s0097-8485(96)80004-0
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发表时间：
1996-03-01
期刊：
影响因子：
--
通讯作者：
Robinson, NL
中科院分区：
文献类型：
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作者：
Gribskov, M;Robinson, NL
本文借鉴临床医学中受试者工作特征（ROC）的思想，将其应用于序列比较。ROC包括敏感性和特异性两个要素，并且是诊断有用性的定量指标。在这项工作中，ROC是用来调查评分表和缺口罚分对数据库搜索的影响。对蛋白质的三个家族，4Fe-4S铁氧化还原蛋白，lysR细菌调节蛋白和细菌RNA聚合酶σ因子的研究得出以下结论：序列家族是相当特异的，但使用Smith-Waterman方法进行数据库搜索的最佳PAM距离比理论方法预测的要大一些，约为200 PAM。与长度无关的空位罚分（空位起始罚分）是相当重要的，但在约20-24的值处显示宽峰。长度依赖性空位罚分（空位延伸罚分）几乎是不相关的，表明成功的数据库搜索仅在有限程度上依赖于空位比对。综上所述，这些观察结果得出的结论是，比对和数据库搜索的最佳条件是不一样的，也不应该期望是一样的。
In this paper, we borrow the idea of the receiver operating characteristic (ROC) from clinical medicine and demonstrate its application to sequence comparison. The ROC includes elements of both sensitivity and specificity, and is a quantitative measure of the usefulness of a diagnostic. The ROC is used in this work to investigate the effects of scoring table and gap penalties on database searches. Studies on three families of proteins, 4Fe-4S ferredoxins, lysR bacterial regulatory proteins, and bacterial RNA polymerase sigma-factors lead to the following conclusions: sequence families are quite idiosyncratic, but the best PAM distance for database searches using the Smith-Waterman method is somewhat larger than predicted by theoretical methods, about 200 PAM. The length independent gap penalty (gap initation penalty) is quite important, but shows a broad peak at values of about 20-24. The length dependent gap penalty (gap extension penalty) is almost irrelevant suggesting that successful database searches rely only to a limited degree on gapped alignments. Taken together, these observations lead to the conclusion that the optimal conditions for alignments and database searches are not, and should not be expected to be, the same.