Domainoid: domain-oriented orthology inference
Domainoid: domain-oriented orthology inference
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DOI：
10.1186/s12859-019-3137-2
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发表时间：
2019-10-28
影响因子：
3
通讯作者：
Sonnhammer, Erik L. L.
中科院分区：
文献类型：
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作者：
Persson, Emma;Kaduk, Mateusz;Sonnhammer, Erik L. L.
背景：同源推断通常是基于全长蛋白质序列。然而，大多数蛋白质包含独立折叠和重复的区域，结构域。蛋白质的结构域结构对其功能至关重要，重组事件意味着单个结构域可能具有不同的进化历史。以前的研究表明，同源蛋白在结构域结构上可能不同，这给全长序列上的同源推断方法带来了挑战。我们开发了Domainoid，这是一个新的工具，旨在通过在域水平上推断正字法来克服全长正字法所面临的这些挑战。它分别在单个域上使用InParanoid算法，来推断出相应域的组。结果：这种面向结构域的方法允许检测不一致的结构域同源物，即同一蛋白质的不同结构域具有不同的进化历史的情况。除了结构域水平分析之外，基于同源结构域的比例可以推断蛋白质水平的同源性。将Domainoid orthology赋值与传统的全长方法InParanoid的赋值进行比较，并在标准基准测试中进行验证。结论：我们的研究结果表明，基于域的同源推断可以揭示许多全长序列方法无法发现的同源关系。
Background: Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains.Results: This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories. In addition to domain level analysis, protein level orthology based on the fraction of domains that are orthologous can be inferred. Domainoid orthology assignments were compared to those yielded by the conventional full-length approach InParanoid, and were validated in a standard benchmark.Conclusions: Our results show that domain-based orthology inference can reveal many orthologous relationships that are not found by full-length sequence approaches.