PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
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DOI：
10.1038/npre.2010.4784.1
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发表时间：
2010-08
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通讯作者：
Michael F. Lin;Irwin Jungreis;Manolis Kellis
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作者：
Michael F. Lin;Irwin Jungreis;Manolis Kellis
由于高通量转录组测序为许多物种中的新型转录物提供了证据，因此重新需要准确的方法来将小的基因组区域分类为蛋白质编码或非编码。我们提出了PhyloCSF，一种新的比较基因组学方法，分析多物种的核苷酸序列比对，以确定它是否可能代表一个保守的蛋白质编码区，基于系统发育密码子模型的正式统计比较。我们表明，PhyloCSF的分类性能在12-speciesDrosophilagenome比对超过所有其他方法，我们在以前的研究中进行了比较，我们提供了一个软件实现供社区使用。我们预计，这种方法将广泛适用于许多其他物种，组织和亚细胞区室的转录组测序，特别是在ENCODE和modENCODE的背景下。
As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-speciesDrosophilagenome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE.