Metrics for comparing regulatory sequences on the basis of pattern counts
Metrics for comparing regulatory sequences on the basis of pattern counts
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DOI：
10.1093/bioinformatics/btg425
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发表时间：
2004-02-12
期刊：
影响因子：
5.8
通讯作者：
van Helden, J
中科院分区：
文献类型：
--
作者：
van Helden, J
动机：上游序列包含短基序，通过特异性结合不同的转录因子介导转录调控。在两个基因的调控区域中存在共同的基序可能被认为是潜在的共同调控的线索。因此，序列之间基于模式计数的（非）相似性度量可用于根据其假定的调控特性对基因进行分类。结果：我们在这里提出了几个依赖于概率论的度量，其目的是在模式计数的基础上比较序列。我们将这些指标与几种经典的不相似性和相似性指标进行比较，并以生物实例说明它们的行为。
Motivation: Upstream sequences contain short motifs, which mediate transcriptional regulation by specifically binding different transcription factors. The presence of common motifs in the regulatory regions of two genes might be considered as a clue for a potential co-regulation. A pattern count-based (dis)similarity metric between sequences could thus be used to classify genes according to their putative regulatory properties.Results: We present here several metrics which rely on probability theory, and which aim at comparing sequences on the basis of pattern counts. We compare these metrics to several classical dissimilarity and similarity metrics, and illustrate their behaviour with a biological example.