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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA.
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EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA.

机译：EVOPRINTER，一种用于快速鉴定功能重要DNA的多基因组比较工具。

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摘要

Here, we describe a multigenomic DNA sequence-analysis tool, evoprinter, that facilitates the rapid identification of evolutionary conserved sequences within the context of a single species. The evoprinter output identifies multispecies-conserved DNA sequences as they exist in a reference DNA. This identification is accomplished by superimposing multiple reference DNA vs. test-genome pairwise blat (blast-like alignment tool) readouts of the reference DNA to identify conserved nucleotides that are shared by all orthologous DNAs. evoprinter analysis of well characterized genes reveals that most, if not all, of the conserved sequences are essential for gene function. For example, analysis of orthologous genes that are shared by many vertebrates identifies conserved DNA in both protein-encoding sequences and noncoding cis-regulatory regions, including enhancers and mRNA microRNA binding sites. In Drosophila, the combined mutational histories of five or more species affords near-base pair resolution of conserved transcription factor DNA-binding sites, and essential amino acids are revealed by the nucleotide flexibility of their codon-wobble position(s). Conserved small peptide-encoding genes, which had been undetected by conventional gene-prediction algorithms, are identified by the codon-wobble signatures of invariant amino acids. Also, evoprinter allows one to assess the degree of evolutionary divergence between orthologous DNAs by highlighting differences between a selected species and the other test species.
机译：在这里，我们描述了一种多基因组DNA序列分析工具evoprinter，它有助于在单个物种的上下文中快速识别进化保守序列。当参考DNA中存在多物种保守的DNA序列时，evoprinter输出将识别它们。通过将参考DNA的多个参考DNA与测试基因组成对blat（blast样比对工具）读数进行叠加，以识别所有直系同源DNA共有的保守核苷酸，可以完成这种鉴定。对特征明确的基因进行的evoprinter分析表明，大多数（如果不是全部）保守序列对于基因功能至关重要。例如，对许多脊椎动物共有的直系同源基因的分析可在蛋白质编码序列和非编码顺式调节区域（包括增强子和mRNA microRNA结合位点）中识别出保守的DNA。在果蝇中，五个或更多物种的组合突变历史提供了保守的转录因子DNA结合位点的近碱基对解析，并且必需氨基酸通过其密码子摆动位置的核苷酸柔韧性得以揭示。保守的小肽编码基因，通过常规氨基酸预测算法尚未发现，可通过不变氨基酸的密码子摆动特征来识别。同样，evoprinter可以通过突出选择的物种与其他测试物种之间的差异来评估直系同源DNA之间进化差异的程度。

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