NGS Overlap Searcher

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Visual analysis of next-generation sequencing data to detect overlapping genes in bacterial genomes

Next generation sequencing (NGS) technologies are about to revolutionize biological research. Being able to sequence large amounts of DNA or, indirectly, RNA sequences in a short time period opens numerous new possibilities. However, analyzing the large amounts of data generated in NGS is a serious challenge, which requires novel data analysis and visualization methods to allow the biological experimenter to understand the results. This new system deals with the flood of data generated by transcriptome sequencing (RNA-seq) using NGS and it allows the analyzer to get a quick overview of the data, as well as interactively explore interesting regions based on the three important parameters: coverage, transcription, and fit. This system supports the NGS analysis in the following respects: (1) Representation of the coverage sequence in a way that no artifacts are introduced. (2) Easy determination of a fit of an open reading frame (ORF) to a transcript by mapping the coverage sequence directly into the ORF representation. (3) Providing automatic support for finding interesting regions to address the problems that the overwhelming volume of data comes with. (4) Providing an overview representation that allows parameter tuning and enables quick access to interesting areas of the genome.

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Institution: University of Konstanz, Technical University of Munich, Germany

This work has been partly funded by the German Research Society (DFG) under the grant SPP 1395 (Informations-und Kommunikationstheorie in der Molekularbiologie, InKoMBio), project 'Finding new overlapping genes and their theory (FOG-Theory)’.