Technology JCoast

JCoast: a next-generation software tool to explore genomic sequence data

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The substantial amount of heterogeneous DNA sequence data currently generated demand for powerful and sustainable software tools for subsequent analysis and exploration. Processing of the raw data is often done by automatic bioinformatic pipelines using high-performance computer hardware, but finally only human interaction can turn this data into biological knowledge. To facilitate this complex task, software tools are required which allow single users to browse, explore and further analyse the processed data, in best case on standard computer hardware to maintain personal flexibility.

In 2008, the JCoast Software Tool for data mining and comparison of prokaryotic (meta)genomes was developed and recently published (Richter et al. 2008) by the Microbial Genomics Group at the MPI-Bremen. JCoast is a Java-based extension for existing genome projects (databases). The platform-independent design of the JCoast workbench allows the user to access pre-processed data in an easy and highly intuitive way. It offers a viewer to organize and browse the data as well as search tools and statistical analysis for a rapid overview and efficient comparisons. 

However, the field of genomics is quickly evolving due to technological advances followed by emerging user demands. Within the technological platform (subproject 5) of the MIMAS project and in close collaboration with the company Ribocon, JCoast will be extended to fulfil future requirements and facilitate comprehensive analysis of the genomic data generated within the project. The extension includes various new functions related to statistical data analysis and visualization, mapping of genes to metabolic pathways, as well as an interface to the proteomics database Marine2D from the Institute of Marine Biotechnology (IMaB) for data integration. By this, JCoast will allow the scientists of the MIMAS project and beyond, to answer questions of genome enabled ecosystem research in a much more efficient way than currently possible.

 

Reference:

Richter M et al. (2008) JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta) genomes. BMC Bioinformatics 9:177