PIRSF: family classification system at the Protein Information Resource
PIRSF: family classification system at the Protein Information Resource
复制标题
DOI：
10.1093/nar/gkh097
复制
发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Barker, WC
中科院分区：
文献类型：
--
作者：
Wu, CH;Nikolskaya, A;Barker, WC
蛋白质信息资源（PIR）是一个完整的蛋白质信息学公共资源。为了促进蛋白质注释的合理传播和标准化以及注释错误的系统检测，PIR扩展了其超家族概念并开发了SuperFamily（PIRSF）分类系统。基于整个蛋白质的进化关系，这种分类系统允许注释特定的生物学和一般的生化功能。该系统采用网络结构，从超家族到亚家族水平进行蛋白质分类。蛋白质家族成员是同源的（共享共同的祖先）和同胚的（共享具有共同结构域架构的全长序列相似性）。PIRSF数据库由两个数据集组成，初步集群和策展家庭。所策划的家族包括家族名称、蛋白质成员、亲子关系、域架构以及可选的描述和参考书目。PIRSF可从网站http://pir.georgetown.edu/pirsf/获得，用于报告检索和序列分类。该报告提供了家族注释，成员统计，与其他数据库的交叉引用，域架构的图形显示，以及与策划家族的多序列比对和系统发育树的链接。PIRSF可以用来分析系统发育概况，揭示功能的收敛和发散，并确定同胚家庭，域和结构类之间的有趣的关系。
The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.