Efficient inference of homologs in large eukaryotic pan-proteomes.
Efficient inference of homologs in large eukaryotic pan-proteomes.
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DOI：
10.1186/s12859-018-2362-4
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发表时间：
2018-09-26
影响因子：
3
通讯作者：
Smit S
中科院分区：
文献类型：
--
作者：
Sheikhizadeh Anari S;de Ridder D;Schranz ME;Smit S
同源基因的鉴定是比较基因组学、功能基因组学和系统基因组学的基础。广泛的公共同源数据库对于研究同源性具有重要价值，但需要不断更新以纳入新序列。随着新序列的快速产生，需要有效的独立工具来检测新数据中的同源物。为了解决这个问题，我们提出了一种快速方法来检测大量个体和/或物种的同源组。我们采用了基于 k-mer 的方法，该方法在不牺牲灵敏度的情况下大大减少了成对蛋白质比对的数量。我们证明了所提出的检测细菌、真菌、植物和后生动物大型蛋白质组同源性的方法的准确性、可扩展性、效率和适用性。我们清楚地观察到同源推理中召回率和精确度之间的权衡。支持召回率或精度在很大程度上取决于应用程序。我们的程序的聚类行为可以通过更改一些关键参数来针对特定应用进行优化。该程序可在 https://github.com/sheikhizadeh/pantools 上供公众使用，作为我们的泛基因组分析工具 PanTools 的扩展。本文的在线版本 (10.1186/s12859-018-2362-4) 包含补充材料，可供授权用户使用。
Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data. To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa. We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at https://github.com/sheikhizadeh/pantools as an extension to our pan-genomic analysis tool, PanTools. The online version of this article (10.1186/s12859-018-2362-4) contains supplementary material, which is available to authorized users.
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