Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes.
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes.
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DOI：
10.1186/s12864-017-4079-6
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发表时间：
2017-08-31
期刊：
影响因子：
4.4
通讯作者：
Lee SF
中科院分区：
文献类型：
--
作者：
Rane RV;Oakeshott JG;Nguyen T;Hoffmann AA;Lee SF
区分多个物种基因之间的直系同源和寄生关系对于比较基因组分析至关重要。已经开发出各种计算方法来解决这些进化关系，但是直系同源预测的精确和回忆之间的强大权衡仍然是一个持续的挑战。
在这里，我们提出了正直预测管道的正形组，旨在降低直系同源捕获率（回忆）和多物种直系同源预测的准确性之间的权衡。该管道比较序列域，然后在使用系统发育比较之前形成序列相似的簇来识别内部分析。然后，它使用新的评分度量捕获全长和碎片基因之间的关系来纠正片段和基因长度偏置的序列相似性指标。然后将其余的基因聚集在一起，以鉴定系统发育框架内的直系同源物。直系同源的预测与内谱和基因出生一起使用同步，以识别新的直系同源关系。我们使用12种高质量的果蝇基因组来表明，与其他直系同源预测管道相比，正形组提供的正群具有最小的误差，但召回率很高。此外，正形组对次优组装/注释质量具有弹性，其中包含来自八个其他果蝇物种的基因组草案，但仍可提供> 6500 1：1直系同源物，同时保留了比其他管道更好的准确性和回忆。正统组可作为可搜索的数据库和查询工具以及所有直系同源物的多序列对齐浏览器。基础文档和数据库可在http://www.orthonome.com上访问。
我们证明，与先前发表的管道一起测试时，正骨组成的正交捕获率和准确性和准确性。这项研究还强调了果蝇物种的进化保护程度要比以前的想法更大。
本文的在线版本（10.1186/S12864-017-4079-6）包含补充材料，可供授权用户使用。
Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue prediction remains an ongoing challenge. Here we present Orthonome, an orthologue prediction pipeline, designed to reduce the trade-off between orthologue capture rates (recall) and accuracy of multi-species orthologue prediction. The pipeline compares sequence domains and then forms sequence-similar clusters before using phylogenetic comparisons to identify inparalogues. It then corrects sequence similarity metrics for fragment and gene length bias using a novel scoring metric capturing relationships between full length as well as fragmented genes. The remaining genes are then brought together for the identification of orthologues within a phylogenetic framework. The orthologue predictions are further calibrated along with inparalogues and gene births, using synteny, to identify novel orthologous relationships. We use 12 high quality Drosophila genomes to show that, compared to other orthologue prediction pipelines, Orthonome provides orthogroups with minimal error but high recall. Furthermore, Orthonome is resilient to suboptimal assembly/annotation quality, with the inclusion of draft genomes from eight additional Drosophila species still providing >6500 1:1 orthologues across all twenty species while retaining a better combination of accuracy and recall than other pipelines. Orthonome is implemented as a searchable database and query tool along with multiple-sequence alignment browsers for all sets of orthologues. The underlying documentation and database are accessible at http://www.orthonome.com. We demonstrate that Orthonome provides a superior combination of orthologue capture rates and accuracy on complete and draft drosophilid genomes when tested alongside previously published pipelines. The study also highlights a greater degree of evolutionary conservation across drosophilid species than earlier thought. The online version of this article (10.1186/s12864-017-4079-6) contains supplementary material, which is available to authorized users.
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