The metabolic SearcH And Reconstruction Kit\ud (metaSHARK) is a new fully automated software package\ud for the detection of enzyme-encoding genes\ud within unannotated genome data and their visualization\ud in the context of the surrounding metabolic network.\ud The gene detection package (SHARKhunt) runs\ud on a Linux systemand requires only a set of raw DNA\ud sequences (genomic, expressed sequence tag and/\ud or genome survey sequence) as input. Its output\ud may be uploaded to our web-based visualization\ud tool (SHARKview) for exploring and comparing data\ud from different organisms. We first demonstrate the\ud utility of the software by comparing its results for\ud the raw Plasmodium falciparum genome with the\ud manual annotations available at the PlasmoDB and\ud PlasmoCyc websites. We then apply SHARKhunt to\ud the unannotated genome sequences of the coccidian\ud parasite Eimeria tenella and observe that, at an\ud E-value cut-off of 10(-20), our software makes 142\ud additional assertions of enzymatic function compared\ud with a recent annotation package working\ud with translated open reading frame sequences. The\ud ability of the software to cope with low levels of\ud sequence coverage is investigated by analyzing\ud assemblies of the E.tenella genome at estimated\ud coverages from 0.5x to 7.5x. Lastly, as an example\ud of how metaSHARK can be used to evaluate the\ud genomic evidence for specific metabolic pathways,\ud we present a study of coenzyme A biosynthesis in\ud P.falciparum and E.tenella
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