PHROG: families of prokaryotic virus proteins clustered using remote homology.
PHROG: families of prokaryotic virus proteins clustered using remote homology.
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PHROG：利用远程同源性聚类原核病毒蛋白的家族。
DOI：
10.1093/nargab/lqab067
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发表时间：
2021-09
影响因子：
4.6
通讯作者：
Enault F
中科院分区：
文献类型：
--
作者：
Terzian P;Olo Ndela E;Galiez C;Lossouarn J;Pérez Bucio RE;Mom R;Toussaint A;Petit MA;Enault F
病毒是丰富、多样和古老的生物实体。它们的多样性很高，无论是在遇到的不同蛋白质家族的数量和每个蛋白质家族的序列异质性方面。最近增加的测序病毒基因组构成了一个很好的机会，以获得新的见解，这种多样性，因此敦促注释资源的发展，以帮助功能和比较分析。在这里，我们介绍PHROG（Propylenic Virus Remote Homologous Groups），一个病毒蛋白质家族库，该病毒蛋白质家族库使用一种新的聚类方法，基于HMM轮廓-轮廓比较的远程同源性检测。考虑原核生物的17473种参考（原）病毒，总共938864种蛋白质中的868340种被分组为38880个簇，这被证明是比使用基于类似BLAST相似性搜索的经典策略的2倍更深的聚类，但尚未保持同质性。人工检查与各种参考序列数据库的相似性，得到5108个簇（包含总蛋白质数据集的50.6%）的注释，其中705个不同的注释术语包括在9个功能类别中，专门为病毒设计。希望PHROG将是一个有用的工具，以更好地注释未来的原核病毒序列，从而帮助科学界更好地了解这些实体的进化和生态。
Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.