FFAS server: novel features and applications.
FFAS server: novel features and applications.
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DOI：
10.1093/nar/gkr441
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发表时间：
2011-07
影响因子：
14.9
通讯作者：
Godzik A
中科院分区：
文献类型：
--
作者：
Jaroszewski L;Li Z;Cai XH;Weber C;Godzik A
Fold and Function Assignment System（FFAS）服务器[Jaroszewski等人（2005）FFAS 03：a server for profile-profile sequence alignment. Nucleic Acids Research，33，W284-W288]实现了最初在[Ryanewski等人，（2000）Comparison of sequence profiles.利用序列信息进行结构预测的策略。Protein Science：a Publication of the Protein Society，9，232-241].在这里，我们将介绍自2005年以来添加到服务器的更新，更改和新功能，并讨论其新应用程序。用于计算序列谱的序列数据库通过添加公开可用的宏基因组序列的集合来富集。用户的蛋白质图谱现在可以与2000多个其他图谱数据库进行比较，包括几个完整的蛋白质组、涉及遗传疾病的人类蛋白质和微生物毒力因子数据库。一个新开发的界面使用一个标签系统，允许用户浏览多个结果页面，还包括新的功能，如点图查看器，建模工具，改进的三维对齐查看器和链接到结构相似性数据库。FFAS服务器还针对速度进行了优化：运行时间减少了一个数量级。FFAS服务器http://ffas.godziklab.org没有登录要求，尽管有一个选项可以在单独的密码保护目录中注册和存储结果。FFAS程序的源代码和Linux可执行文件可从FFAS服务器下载。
The Fold and Function Assignment System (FFAS) server [Jaroszewski et al. (2005) FFAS03: a server for profile–profile sequence alignments. Nucleic Acids Research, 33, W284–W288] implements the algorithm for protein profile–profile alignment introduced originally in [Rychlewski et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science: a Publication of the Protein Society, 9, 232–241]. Here, we present updates, changes and novel functionality added to the server since 2005 and discuss its new applications. The sequence database used to calculate sequence profiles was enriched by adding sets of publicly available metagenomic sequences. The profile of a user’s protein can now be compared with ∼20 additional profile databases, including several complete proteomes, human proteins involved in genetic diseases and a database of microbial virulence factors. A newly developed interface uses a system of tabs, allowing the user to navigate multiple results pages, and also includes novel functionality, such as a dotplot graph viewer, modeling tools, an improved 3D alignment viewer and links to the database of structural similarities. The FFAS server was also optimized for speed: running times were reduced by an order of magnitude. The FFAS server, http://ffas.godziklab.org, has no log-in requirement, albeit there is an option to register and store results in individual, password-protected directories. Source code and Linux executables for the FFAS program are available for download from the FFAS server.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
2.9
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
通讯作者：
Dunbrack, Roland L., Jr.
影响因子：
14.9
作者：
Brandt BW;Heringa J
通讯作者：
Heringa J
DOI：
10.1107/s0907444904010145
发表时间：
2004-07-01
影响因子：
2.2
作者：
Schwarzenbacher, R;Godzik, A;Jaroszewski, L
通讯作者：
Jaroszewski, L
影响因子：
14.8
作者：
Kelley, Lawrence A.;Sternberg, Michael J. E.
通讯作者：
Sternberg, Michael J. E.