QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
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DOI：
10.1093/nar/gki496
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Ben-Tal, N
中科院分区：
文献类型：
--
作者：
Gutman, R;Berezin, C;Wollman, R;Rosenberg, Y;Ben-Tal, N
序列特征数据库如PROSITE，其包括指示蛋白质功能的氨基酸片段，可用于蛋白质注释。遗憾的是，注释并不总是准确的。标签可能在不执行相关功能的蛋白质中被错误地检测到（假阳性预测，FP），或者可能在执行功能的蛋白质中被忽略（假阴性预测，FN）。出现了一种新方法，其中签名被序列图谱取代，该序列图谱是根据具有相同功能的同源蛋白质的多重序列比对（MSA）计算的。这种方法上级于简单模式搜索，基本上是用查询蛋白质的序列对MSA文库进行搜索。我们在这里提出了一种替代方法，在QuasiMotistrom Web服务器（）中实现，该方法基于对原始PROSITE签名的同源查询蛋白质的MSA搜索。与简单模式搜索相比，显式使用查询蛋白质中签名的平均进化保守性显着降低了FP预测的速率。与简单的模式搜索相比，QuasiMotistrial也具有降低的FN预测率，因为对精确签名的传统搜索已经被对物理化学上类似于已知签名的签名样模式的许可搜索所取代。总的来说，QuasiMotivalence和配置文件搜索在性能方面彼此相当。它们也是彼此互补的，因为在一个中被错误检测到（或被忽略）的签名可以被另一个正确检测到。
Sequence signature databases such as PROSITE, which include amino acid segments that are indicative of a protein's function, are useful for protein annotation. Lamentably, the annotation is not always accurate. A signature may be falsely detected in a protein that does not carry out the associated function (false positive prediction, FP) or may be overlooked in a protein that does carry out the function (false negative prediction, FN). A new approach has emerged in which a signature is replaced with a sequence profile, calculated based on multiple sequence alignment (MSA) of homologous proteins that share the same function. This approach, which is superior to the simple pattern search, essentially searches with the sequence of the query protein against an MSA library. We suggest here an alternative approach, implemented in the QuasiMotiFinder web server (), which is based on a search with an MSA of homologous query proteins against the original PROSITE signatures. The explicit use of the average evolutionary conservation of the signature in the query proteins significantly reduces the rate of FP prediction compared with the simple pattern search. QuasiMotiFinder also has a reduced rate of FN prediction compared with simple pattern searches, since the traditional search for precise signatures has been replaced by a permissive search for signature-like patterns that are physicochemically similar to known signatures. Overall, QuasiMotiFinder and the profile search are comparable to each other in terms of performance. They are also complementary to each other in that signatures that are falsely detected in (or overlooked by) one may be correctly detected by the other.
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