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PanGEA: Identification of allele specific gene expression using the 454 technology

Robert Kofler1*, Tatiana Teixeira Torres2, Tamas Lelley1 and Christian Schlötterer2

Author Affiliations

1 University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology, Institute for Plant Production Biotechnology Konrad Lorenz Str 20, A-3430 Tulln, Austria

2 Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Josef Baumann Gasse 1, 1210 Wien, Austria

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BMC Bioinformatics 2009, 10:143  doi:10.1186/1471-2105-10-143

Published: 14 May 2009

Abstract

Background

Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression.

Results

We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technology

Conclusion

To our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: http://www.kofler.or.at/bioinformatics/PanGEA webcite