EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. doi: 10.1093/nar/gky448.
The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.
HMMER 网页服务器（http://www.ebi.ac.uk/Tools/hmmer）是一个免费使用的服务，它使用 HMMER 软件套件（http://hmmer.org）对广泛使用的序列数据库和 Profile Hidden Markov Model (HMM) 库进行快速搜索。序列搜索的结果可以通过多种方式进行总结，允许用户通过结构域或分类学查看和过滤显著命中。对于大规模使用，我们提供了一个应用程序编程接口（API），该接口的范围已经扩大，使得所有的结果表示都可以通过 HTML 和 API 获得。此外，我们还重构了我们的 JavaScript 可视化库，为不同的结果表示提供了独立的组件。这些组件使用上述 API 进行消费，并可以集成到第三方网站中。可以搜索的数据库范围已经扩大，增加了四个序列数据集（总共 12 个）和一个 Profile HMM 库（总共 6 个）。为了帮助用户探索其结果的生物学背景，并发现新的数据资源，现在在搜索结果中补充了到其他 EMBL-EBI 数据库的交叉引用。
