metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella ud

摘要

The metabolic SearcH And Reconstruction Kitud(metaSHARK) is a new fully automated software packageudfor the detection of enzyme-encoding genesudwithin unannotated genome data and their visualizationudin the context of the surrounding metabolic network.udThe gene detection package (SHARKhunt) runsudon a Linux systemand requires only a set of raw DNAudsequences (genomic, expressed sequence tag and/udor genome survey sequence) as input. Its outputudmay be uploaded to our web-based visualizationudtool (SHARKview) for exploring and comparing dataudfrom different organisms. We first demonstrate theudutility of the software by comparing its results forudthe raw Plasmodium falciparum genome with theudmanual annotations available at the PlasmoDB andudPlasmoCyc websites. We then apply SHARKhunt toudthe unannotated genome sequences of the coccidianudparasite Eimeria tenella and observe that, at anudE-value cut-off of 10(-20), our software makes 142udadditional assertions of enzymatic function comparedudwith a recent annotation package workingudwith translated open reading frame sequences. Theudability of the software to cope with low levels ofudsequence coverage is investigated by analyzingudassemblies of the E.tenella genome at estimatedudcoverages from 0.5x to 7.5x. Lastly, as an exampleudof how metaSHARK can be used to evaluate theudgenomic evidence for specific metabolic pathways,udwe present a study of coenzyme A biosynthesis inudP.falciparum and E.tenella.