Team Symbiose

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography

Section: Overall Objectives

Highlights of the year

We have designed a major high performance sequence algorithm for bioinformatics: we propose a very efficient alternative to BLAST for comparing large genomic banks, an issue that becomes increasingly important with the development of high throughput Next Generation Sequencing technologies. The software, called PLAST (Parallel Local Alignment Search Tool), is able to run on a large variety of parallel architectures. Speed-up of X5 are typically observed compared to the multithreaded Blast software, reaching X10 while using GPU boards and X30 with FPGA processing units [22] , [41] .

From the point of view of modelling, we got several results that show the potential of our methods in biology. We have obtained high impact publications on a study on the canalization of gene expression in the Drosophila blastoderm during early development [21] , [20] . This emphasizes the interest of developing precise dynamical models of gene regulations. We have also developed an identification method and database for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regrouping the analysis of all known archeal or bacterial genomes (more than 1100 species). It offers the best reference to date to these elements implied in microbial defense mechanisms [26] .

At the national level, Genouest is the sole Bioinformatics core facility hosted in a computer science laboratory. It received in 2009 a label “IBISA” (IBISA is the coordination structure for the technological platforms dedicated to life science in France) and confirmed its ISO 9001:2000 certification in March. Our collaborations with Inra proved to be very fruitful. One of our highlight software, Biomaj, developed in collaboration with Inra has been downloaded more than a hundred of times. It aims at the management of large scale data workflows and offers a great help to bioinformatics platforms and laboratories that need to automatically update data banks on a regular basis. A national Inria development action has started at the end of the year to reinforce the project. We have also investigated insect genomics, hosting AphidBase, a comprehensive genome information resource dedicated to annotation of the pea aphid genome that is used by the International Aphid Genomics Consortium (IAGC).


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