Description:The European Molecular Biology Open Software Suite in the JST framework
Abstract:EMBOSS, ”The European Molecular Biology Open Software Suite” is a free Open Source software analysis package well established in the world-wide bioinformatics community. The tool has been adapted to be executed on the EGEE grid infrastructure within the JST framework in order to perform large scale analyses. Compared to other porting of the EMBOSS package on the GRID environment such as GrEMBOSS (http://cimi.ccg.unam.mx/ccg-OrganicG/en/GrEMBOSS), a gridified version of EMBOSS developed inside the EELA project, EMBOSS_in_JST appears to be well performing in the management of large data flow. The validity of the EMBOSS_in_JST approach was validated on a case study on Viroids. They are circular RNAs infecting plants. They show compact secondary structures and are unable to code for any protein. Infectivity of these RNAs exclusively relies on their ability to interact directly with host factors (proteins and/or RNAs) and to redirect cellular machinery and biosynthetic pathways for their replication and spread in the host. Viroids accomplish this aim likely mimicking some host RNA structural property. Therefore, viroid RNAs may unveil structural motives with functional properties also contained in cellular RNAs. Bioinformatics approaches in viroid research are impaired by the fact that the complete genome of most natural viroid hosts is still unknown. To overcome this difficulty we decided to run a secondary structure analysis on sub-sequences of the whole plant sequence data set available in EMBL. We analysed as a first test 231’000 intron regions for the secondary structure of interest by using the vrnalfold algorithm (search for local folding patterns) from the EMBOSS/EMBASSY package.