Karro John E, Yan Yangpan, Zheng Deyou, Zhang Zhaolei, Carriero Nicholas, Cayting Philip, Harrrison Paul, Gerstein Mark
Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.
Nucleic Acids Res. 2007 Jan;35(Database issue):D55-60. doi: 10.1093/nar/gkl851. Epub 2006 Nov 11.
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different approaches to the problem of identification. Consequently, it is difficult to maintain a consistent collection of pseudogenes in detail necessary for their effective use. Our database is designed to address this issue. It integrates a variety of heterogeneous resources and supports a subset structure that highlights specific groups of pseudogenes that are of interest to the research community. Tools are provided for the comparison of sets and the creation of layered set unions, enabling researchers to derive a current 'consensus' set of pseudogenes. Additional features include versatile search, the capacity for robust interaction with other databases, the ability to reconstruct older versions of the database (accounting for changing genome builds) and an underlying object-oriented interface designed for researchers with a minimal knowledge of programming. At the present time, the database contains more than 100,000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources.
“假基因.org知识库”是假基因注释的综合存储库。假基因的定义在文献中各不相同，这导致在识别问题上有显著不同的方法。因此，难以维护对其有效使用而言必要的详细、一致的假基因集合。我们的数据库旨在解决这个问题。它整合了各种异构资源，并支持一种子集结构，突出了研究界感兴趣的特定假基因组。提供了用于集合比较和创建分层集合并集的工具，使研究人员能够得出当前的假基因“共识”集。其他功能包括通用搜索、与其他数据库进行强大交互的能力、重建数据库旧版本的能力（考虑到基因组构建的变化）以及为编程知识最少的研究人员设计的底层面向对象接口。目前，该数据库包含跨越64个原核生物和11个真核生物基因组的100,000多个假基因，包括从16个来源汇编的人类注释集合。
