| Genomics disciplines such as genome sequencing, functional genomics, transcriptomics, proteomics, and metabolomics produce vast amounts of biological data that need to be stored, organized, compared, interpreted and translated into knowledge. This field of expertise is called Bioinformatics, and requires an enormous computational capacity to process and analyse huge amounts of data and information. At WCFS, a Bioinformatics working group has been established with members from various projects, who regularly meet to discuss and exchange information on all aspects of new biological databases, software tools, literature and conferences that could provide support for WCFS research. This effort is a collaboration with the Bacterial Genomics group of the Center for Molecular and Biomolecular Informatics, University of Nijmegen (www.cmbi.kun.nl). Objectives and deliverables Our goals are to provide bioinformatics support to all WCFS projects, in particular for the Programme 3 on Microbial Functionality and Safety. This involves direct analysis of large data sets, development and integration of databases, and development and use of software tools for data analysis. Public and commercial databases and software tools are assessed, and where necessary implemented and integrated. Scientific progress In 2003, bioinformatics support was provided to several projects. The complete genome sequence of Lactobacillus plantarum WCFS1 and detailed annotation of the coding potential was published (Kleerebezem et al, 2003). A detailed comparative analysis of encoded prophages was performed in collaboration with Nestle Research Center, Lausanne (Ventura et al, 2003). The first version of a model of the metabolic pathways present in Lb. plantarum was constructed using the high quality annotated genome data: LacPlantCyc, pathway reconstruction in Lb. plantarum. Various in-house databases have been developed, such as PlantDB (annotation of L.plantarum), PlantaReg (regulators of L.plantarum), and MotifDB (transcription factor binding motifs). In the context of the IOP-comparative genomics project, a web-based tool was developed, the Microbial GenomeViewer (www.cmbi.kun.nl/MGV), for interactive visualization of genome annotation and transcriptome data. Related activities In collaboration with the Center for Molecular and Biomolecular Informatics, University of Nijmegen, our bioinformatics activities related to WCFS projects include the IOP-comparative genomics project (IGE01018), the NWO-Bioinformatics project on Computational genomics of prokaryotes (050.50.206) and support for the Kluyver Centre activities. |
