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；

基本信息

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

项目摘要

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.

在过去几年中开发的新技术大大增加了实验室生产的生物序列信息的量。结果，现在有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尚未由科学家检查，也没有任何实验信息来暗示其功能可能是什么。 PFAM和INTERPRO资源有助于使用概率模型通过检查其氨基酸序列来预测蛋白质的功能。 PFAM可以说是此类模型中最著名的生产商之一。同时，InterPro不会直接产生模型，而是从PFAM和其他10个补充数据库中获取它们，将它们集成在一起并添加功能信息。国际螺旋体定期与蛋白质序列的主要公共存储库的完整内容（Uniprot知识库），以便可以转移其功能预测。为了使InterPro和PFAM可以继续涵盖序列的序列数量不断增长，并保持准确的序列并保持准确性。预测，需要制定和集成新的模型，需要检查现有模型及其匹配的蛋白质。该项目的目的之一是支持这项工作。另一个目的是查看PFAM或INTERPRO当前未使用的其他预测方法，这些方法识别蛋白质序列中蛋白质功能的蛋白质序列中的单个氨基酸。我们将将此功能添加到资源中，并使用它使他们的预测更加准确。反过来，这将提高与Uniprot知识库中大量蛋白质相关的信息质量。以这种方式增加资源将需要更改一些基础软件。同时，我们将更新InterPro和PFAM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，以向新用户介绍资源，并向现有用户提供有关新功能的新用户。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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.