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Scientific Programmes: Structural Biology and Biocomputing Programme >
National Bioinformatics Institute Unit
Scientific Programmes
Structural Biology and Biocomputing Programme
National Bioinformatics Institute Unit
Head of Unit:
Alfonso Valencia
Overview Last update May/2010
During 2009 the INB Unit has continued to develop the MADAS and CARGO systems:
- MADAS is a sequence annotation system integrating database and user data. The system is being used in the European pSYSMO and EMERGENCE projects.
- CARGO is a confi gurable biological web portal designed to facilitate, integrate, and visualise functional information associated to gene lists derived from cancer genome studies.
The INB function annotation toolkit includes the following systems:
- FUNCUT, an application for functional annotation of complete protein families with emphasis on sub-family differences including GO terms.
- TreeDet, a set of methods for the prediction of functional sites based on sequence information.
- FireDB/FireStar, a database and web interface for the extrapolation of binding sites from known protein structures.
- APRIS, a system for the annotation of principal splicing variants, developed under the ENCODE project.
- BioCreative Metaserver (BCMS), a text system able to annotate protein interactions in biological text by collecting text-mining results from distributed servers.
- GOPHER, a system to handle the automatic evaluation of bioiformatics methods. This fi rst implementation addresses the evaluation of function prediction systems. In the future the system will be extended to the evaluation of bioinformatics methods in other areas.
In the area of Databases the INB Unit is developing PANGENES – an application to handle cancer epidemiological information developed in collaboration with the CNIO Genetic and Molecular Epidemiology Group, as well as the database to manage the results of the Spanish International Cancer Genome Consortium project.
Finally, the INB Unit has transferred a collection of more than 400 INB web services to the European EMBRACE registry, the embrion of the future European bioinformatics core infrastructure in this area.
