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Open Access Software

PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

Csaba Ortutay1 and Mauno Vihinen12*

Author Affiliations

1 Institute of Medical Technology, University of Tampere, FI-33014 Tampere, Finland

2 Research Unit, Tampere University Hospital, FI-33520 Tampere, Finland

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BMC Bioinformatics 2008, 9:299  doi:10.1186/1471-2105-9-299

Published: 2 July 2008

Abstract

Background

Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes as well as novel genes and gene fragments.

Description

The service can detect pseudogenes, that have arisen either by retrotransposition or segmental genome duplication, many of which are not listed in the public pseudogene databases. The service has a user-friendly web interface and uses a powerful computer cluster in order to perform parallel searches and provide relatively fast runtimes despite exhaustive database searches and analyses.

Conclusion

PseudoGeneQuest is a versatile tool for detecting novel pseudogene candidates from the human genome. The service searches human genome sequences for five types of pseudogenes and provides an output that allows easy further analysis of observations. In addition to the result file the system provides visualization of the results linked to Ensembl Genome Browser. PseudoGeneQuest service is freely available.