Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
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DOI：
10.1093/bioinformatics/btn004
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发表时间：
2008-03-01
期刊：
影响因子：
5.8
通讯作者：
Pereira, Fernando C. N.
中科院分区：
文献类型：
--
作者：
Liu, Qian;Mackey, Aaron J.;Pereira, Fernando C. N.
动机：越来越多的多样性和可变质量的相关基因注释的证据主张一个概率框架，自动集成这样的证据，以产生候选基因models.Results：Evigan是一个自动化的基因注释程序真核生物基因组，采用概率推理整合多个来源的基因证据。概率模型是一个动态贝叶斯网络，其参数被调整以最大化观察到的证据的概率。然后，通过最大似然解码得到一致基因预测，产生n个最佳模型（每个模型具有概率）。Evigan能够适应各种证据类型，包括（但不限于）由不同基因发现者计算的基因模型，BLAST命中，EST匹配和剪接位点预测;学习参数编码证据来源的相对质量。由于不需要单独的训练数据（除了个别基因发现者使用的训练集之外），Evigan对于新测序的基因组特别有吸引力，因为这些基因组很少或没有可靠的手动管理注释。产生备选基因模型的排序列表的能力可以促进备选剪接转录物的鉴定。实验应用到人类基因组的ENCODE区域，以及间日疟原虫和拟南芥的基因组表明，Evigan比用作证据的任何单个数据源都获得了更好的性能。
Motivation: The increasing diversity and variable quality of evidence relevant to gene annotation argues for a probabilistic framework that automatically integrates such evidence to yield candidate gene models.Results: Evigan is an automated gene annotation program for eukaryotic genomes, employing probabilistic inference to integrate multiple sources of gene evidence. The probabilistic model is a dynamic Bayes network whose parameters are adjusted to maximize the probability of observed evidence. Consensus gene predictions are then derived by maximum likelihood decoding, yielding n-best models (with probabilities for each). Evigan is capable of accommodating a variety of evidence types, including (but not limited to) gene models computed by diverse gene finders, BLAST hits, EST matches, and splice site predictions; learned parameters encode the relative quality of evidence sources. Since separate training data are not required (apart from the training sets used by individual gene finders), Evigan is particularly attractive for newly sequenced genomes where little or no reliable manually curated annotation is available. The ability to produce a ranked list of alternative gene models may facilitate identification of alternatively spliced transcripts. Experimental application to ENCODE regions of the human genome, and the genomes of Plasmodium vivax and Arabidopsis thaliana show that Evigan achieves better performance than any of the individual data sources used as evidence.