• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Nucleic acids research >PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features
【24h】

PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

机译：PASS2数据库，用于对远距离相关的SCOP域超家族进行基于结构的序列比对：更新至版本5和新增的功能

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/.
机译：基于结构的序列比对是评估和分析远距离相关蛋白之间关系的重要步骤。 PASS2是一个数据库，记录了蛋白质结构域超家族的此类比对，并且已定期进行定期更新。 PASS2版本的此更新名为PASS2.5，直接对应于SCOPe 2.04版本。包括少于40％序列同一性的所有SCOPe结构域，如蛋白质结构的ASTRAL纲要所定义。当前版本包括1977个超家族，并已使用基于结构的序列比对协议进行组装。首先通过MATT获得这种对齐方式，然后通过COMPARER程序进行优化。 JOY程序已用于此类路线的结构注释。在此更新中，我们已使该协议自动化，并着重使用了新功能，例如GO术语的映射，超家族中域之间绝对保守的残基以及SCOPe 2.04中不存在的PDB，使用了来自超家族成员的排列，并作为单独的列表提供。我们还实现了一种更加用户友好的数据表示方式，并提供了用于下载更多功能的选项。可通过http://caps.ncbs.res.in/pass2/获得PASS2.5版本。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号