Keeping pace with protein sequence annotation; consolidating and enhancing Pfam and InterPro's methodologies for functional prediction

最近几年发展起来的新技术大大增加了实验室可以产生的生物序列信息的数量。因此，现在有非常大且不断增长的序列数据进入公共数据库。这些序列中的绝大多数都没有经过科学家的检验，也没有任何实验信息来说明它们的功能。Pfam和InterPro的资源帮助填补了这一空白，他们使用概率模型通过检查蛋白质的氨基酸序列来预测蛋白质的功能。Pfam可以说是最知名的，也是此类模型最大的生产商之一。与此同时，InterPro并不直接生成模型，而是从Pfam和其他10个互补数据库中获取模型，将它们整合在一起，并添加功能信息。InterPro定期针对蛋白质序列的主要公共存储库UniProt知识库的全部内容运行，以便其功能预测可以转移。为了使InterPro和Pfam能够继续覆盖越来越多的序列并保持预测的准确性，需要制作和整合新的模型，需要检查现有模型并评估它们匹配的蛋白质。该项目的目的之一就是支持这一努力。另一个目标是寻找Pfam和InterPro目前没有使用的其他预测方法，这些方法可以识别蛋白质序列中负责蛋白质功能的单个氨基酸。我们将把这个功能添加到资源中，并使用它使它们的预测更加准确。这将反过来提高与UniProt知识库中大量蛋白质相关的信息的质量。以这种方式添加资源将需要对一些底层软件进行更改。同时，我们将更新InterPro和Pfam网站，以便用户可以方便地看到新的和改进的数据，并了解其含义。最后，我们将准备和组织培训材料和课程，向新用户介绍资源，并向现有用户介绍新的和更新的功能。

New technologies, developed in the last few years, have greatly increased the amount of biological sequence information that it is possible for laboratories to produce. As a result, there is now a very large and ever-growing amount of sequence data entering public databases. The overwhelming majority of these sequences have not been examined by scientists, nor is there any experimental information to suggest what their function might be. The Pfam and InterPro resources help plug this gap, using probabilistic models to predict the function of proteins by examining their amino acid sequences. Pfam is arguably the most well-known and one of the largest producers of such models. InterPro, meanwhile, does not produce models directly, but takes them from Pfam and 10 other complementary databases, integrating them together and adding functional information. InterPro is regularly run against the full contents of the main public repository for protein sequences, the UniProt Knowledgebase, so that its functional predictions can be transferred.In order that InterPro and Pfam can continue to cover the growing number of sequences and remain accurate in their predictions, new models need to be made and integrated, existing models need to be checked and the proteins that they match evaluated. One aim of the project is to support this effort. Another aim is to look at other prediction methods, not currently used by either Pfam or InterPro, that identify the individual amino acids in a protein sequence that are responsible for the protein's functions. We will add this functionality to the resources and use it to make their predictions more accurate. This will in turn improve the quality of information associated with large numbers of proteins in the UniProt Knowledgebase. Adding to the resources in this way will require changes to some of the underlying software. At the same time, we will update the InterPro and Pfam web sites, so that users can easily see the new and improved data, and understand what it means. Finally, we will prepare and organise training materials and courses to introduce new users to the resources and educate existing users about the new and updated features.