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

与蛋白质序列注释保持同步；

• 批准号: BB/L024136/1
• 负责人: Alex Bateman
• 金额: $ 69.49万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL024136%2F1
• 关键词: Keeping; pace; protein; sequence; annotation

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.

过去几年发展的新技术极大地增加了实验室可能产生的生物序列信息量。因此，现在有非常大量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还没有被科学家研究过，也没有任何实验信息表明它们的功能可能是什么。Pfam和InterPro资源有助于填补这一空白，它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可以说是这类车型最知名、最大的生产商之一。与此同时，InterPro并不直接制作模型，而是从Pfam和其他10个互补的数据库中提取模型，将它们集成在一起，并添加功能信息。InterPro定期根据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能够继续涵盖不断增长的序列数量并保持预测的准确性，需要建立新的模型并进行集成，需要检查现有模型并评估它们匹配的蛋白质。该项目的一个目标是支持这一努力。另一个目标是寻找目前Pfam或InterPro都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个别氨基酸。我们将向资源添加此功能，并使用它来使他们的预测更准确。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的网站，以便用户可以轻松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，向新用户介绍这些资源，并向现有用户介绍新功能和最新功能。

项目成果

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.

• DOI: 10.1093/bib/bbu053
• 发表时间: 2015-09
• 期刊: Briefings in bioinformatics
• 影响因子: 9.5
• 作者: Chiang Z;Vastermark A;Punta M;Coggill PC;Mistry J;Finn RD;Saier MH Jr
• 通讯作者: Saier MH Jr

The Pfam protein families database: towards a more sustainable future.

• DOI: 10.1093/nar/gkv1344
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Finn RD;Coggill P;Eberhardt RY;Eddy SR;Mistry J;Mitchell AL;Potter SC;Punta M;Qureshi M;Sangrador-Vegas A;Salazar GA;Tate J;Bateman A
• 通讯作者: Bateman A

InterPro in 2017-beyond protein family and domain annotations.

• DOI: 10.1093/nar/gkw1107
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Finn RD;Attwood TK;Babbitt PC;Bateman A;Bork P;Bridge AJ;Chang HY;Dosztányi Z;El-Gebali S;Fraser M;Gough J;Haft D;Holliday GL;Huang H;Huang X;Letunic I;Lopez R;Lu S;Marchler-Bauer A;Mi H;Mistry J;Natale DA;Necci M;Nuka G;Orengo CA;Park Y;Pesseat S;Piovesan D;Potter SC;Rawlings ND;Redaschi N;Richardson L;Rivoire C;Sangrador-Vegas A;Sigrist C;Sillitoe I;Smithers B;Squizzato S;Sutton G;Thanki N;Thomas PD;Tosatto SC;Wu CH;Xenarios I;Yeh LS;Young SY;Mitchell AL
• 通讯作者: Mitchell AL

Gene Ontology Consortium: going forward.

• DOI: 10.1093/nar/gku1179
• 发表时间: 2015-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Gene Ontology Consortium

The Gene Ontology resource: enriching a GOld mine.

• DOI: 10.1093/nar/gkaa1113
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Gene Ontology Consortium