Section: New Software and Platforms

Shogen

Keywords: Systems Biology - Bioinformatics - Genomics

Functional Description

This ASP-based software aims at identifying every segments of consecutive genes in a bacterial genome with a maximum number of genes that participates in a given metabolic pathway. Through this selection, the shogen tool deciphers putative sets of genes that (1) take an active part in metabolic pathways while being closely connected via metabolic networks and (2) are consecutive on each of the genomes involved. In practice, our approach connects genomic and metabolic knowledge by considering the genome organization and the biochemical reactions catalyzed by enzymes encoded by its genes. The underline parsimonious principle assumes that genes must be jointly regulated to activate a metabolic reaction cascade, and should be close enough in the genome organization. In 2015, the tool was simplified to handle standardized data formats, enabling its application to the modelling of a bacterial community [17]

• Participants: Philippe Bordron, Damien Eveillard, Alejandro Maass and Anne Siegel

• Partners: LINA - University of Chile

• Contact: Anne Siegel

• URL: http://aspforbiology.genouest.org/wiki.php/Software%20&%20Biological%20applications