PseudoGeneQuest - service for identification of different pseudogene types in the human genome

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.

Figure 1

Layout of the PseudoGeneQuest service. The user initiates the search by providing a protein sequence on the web page. The analysis is performed on a cluster using databases, search programs and scripts. The results are mailed to the user, and deposited on the web server, where they can be accessed with the provided search ID.

Figure 2

Overview of the search algorithm of PseudoGeneQuest service. User provides the protein query sequence and the number of best hits wanted. The algorithm provides seven types of results in addition to the known genes and pseudogenes (see Table 1). The chart is a modified version of Figure 1 from [9].