An automatic method for identifying surface proteins in bacteria: SLEP
1 Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University. 00185 Rome, Italy
2 Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, Italy
3 CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita' e Ricerca, 00185 Rome, Italy
4 Istituto Pasteur Fondazione Cenci - Bolognetti, Sapienza University. 00185 Rome, Italy
BMC Bioinformatics 2010, 11:39 doi:10.1186/1471-2105-11-39Published: 20 January 2010
Bacterial infections represent a global health challenge. The identification of novel antibacterial targets for both therapy and vaccination is needed on a constant basis because resistance continues to spread worldwide at an alarming rate. Even infections that were once easy to treat are becoming difficult or, in some cases, impossible to cure. Ideal targets for both therapy and vaccination are bacterial proteins exposed on the surface of the organism, which are often involved in host-pathogen interaction. Their identification can greatly benefit from technologies such as bioinformatics, proteomics and DNA microarrays.
Here we describe a pipeline named SLEP (Surface Localization Extracellular Proteins), based on an automated optimal combination and sequence of usage of reliable available tools for the computational identification of the surfome, i.e. of the subset of proteins exposed on the surface of a bacterial cell.
The tool not only simplifies the usage of these methods, but it also improves the results by selecting the specifying order and combination of the instruments. The tool is freely available at http://www.caspur.it/slep webcite.