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

Content Provider	PubMed Central
Author	Pinney, John W. Shirley, Martin W. Mcconkey, Glenn A. Westhead, David R.
Copyright Year	2005
Abstract	The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux system and requires only a set of raw DNA sequences (genomic, expressed sequence tag and/or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10−20, our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5× to 7.5×. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella.
Related Links	http://dx.doi.org/10.1093/nar/gki285
Starting Page	1399
File Format	PDF
ISSN	13624962
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	4
Volume Number	33
Language	English
Publisher	Oxford University Press
Publisher Date	2005-01-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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