PanGEA: identification of allele specific gene expression using the 454 technology.
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


CONCLUSIONS
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
University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology, Institute for Plant Production Biotechnology Konrad Lorenz Str 20, A-3430 Tulln, Austria. robert@kofler.or.at
Robert
R
Kofler
Tatiana
T
Teixeira Torres
Tamas
T
Lelley
Christian
C
Schlötterer
D000483:Alleles; D001483:Base Sequence; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software