HMM Logos for visualization of protein families -: art. no. 7
HMM Logos for visualization of protein families -: art. no. 7
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DOI：
10.1186/1471-2105-5-7
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发表时间：
2004-01-21
影响因子：
3
通讯作者：
Rahmann, S
中科院分区：
文献类型：
--
作者：
Schuster-Böckler, B;Schultz, J;Rahmann, S
背景：剖面隐藏的马尔可夫模型（PHMM）是一种用于蛋白质家庭研究的广泛使用的工具。然而，到目前为止，还没有任何方法可以以直观的方式以图形方式以图形方式可视化它们的所有中心方面。回报：我们提出了一种可视化方法，它包含了pHMM的发射和过渡概率，从而扩展了Schneider和Schneider和斯蒂芬斯。对于pHMM的每个发射状态，我们都会显示一堆字母。堆栈高度取决于位置的字母发射频率与背景频率的偏差。堆栈宽度可视化到达状态的概率（命中概率）和国家通过模型期间发出的预期字母数量（州的预期贡献）。可以在Max Planck分子遗传学研究所的徽标Web服务器上找到源代码http：// logos.molgen.mpg.mpg.de.conclusions：我们证明HMM徽标可以是生物学家的有用工具：我们使用它们来使用它们来突出了GTPases，RAB和RAS的两个同源亚家族之间的差异，我们表明它们能够指示RAS的结构元素。
Background: Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way.Results: We present a visualization method that incorporates both emission and transition probabilities of the pHMM, thus extending sequence logos introduced by Schneider and Stephens. For each emitting state of the pHMM, we display a stack of letters. The stack height is determined by the deviation of the position's letter emission frequencies from the background frequencies. The stack width visualizes both the probability of reaching the state ( the hitting probability) and the expected number of letters the state emits during a pass through the model ( the state's expected contribution).A web interface offering online creation of HMM Logos and the corresponding source code can be found at the Logos web server of the Max Planck Institute for Molecular Genetics http:// logos.molgen.mpg.de.Conclusions: We demonstrate that HMM Logos can be a useful tool for the biologist: We use them to highlight differences between two homologous subfamilies of GTPases, Rab and Ras, and we show that they are able to indicate structural elements of Ras.