Database Commons a catalog of biological databases

Database Commons - Pseudogene

Pseudogene

Citations: 115

z-index 1.99

Short name Pseudogene
Full name
Description The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation.
URL https://genome.uiowa.edu/pseudogenes/
Year founded 2007
Last update & version 2007-01-01    v1.0
Availability Not Available
University/Institution hosted Pennsylvania State University
Address University Park, PA 16802, USA
City Pennsylvania
Province/State PA
Country/Region United States
Contact name John E. Karro
Contact email jkarro@acm.org
Data type(s)
Major organism(s)
Keyword(s)
  • pseudogene annotation
Publication(s)
  • Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. [PMID: 17099229]

    John E Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul Harrrison, Mark Gerstein
    Nucleic acids research 2007:35(Database issue)
    115 Citations (Google Scholar as of 2016-04-29)

    Abstract: 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.

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Tags

DNA
Homo sapiens
pseudogene annotation

Record metadata

  • Created on: 2015-08-10
  • Curated by:
    • Shixiang Sun [2015-11-22]
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