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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

Pinney, J.W., Shirley, M.W., McConkey, G.A. and Westhead, D.R. (2005) metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Research, 33 (4). pp. 1399-1409. ISSN 1362-4962

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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 systemand 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 0.5x to 7.5x. 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.

Item Type: Article
Copyright, Publisher and Additional Information: © 2005, the authors. Published by Oxford University Press.
Keywords: cuticle, cracking, epidermis, fruit growth, Lycopersicon esculentum, plant biomechanics, ripening, stiffening, tomato
Institution: The University of Leeds
Academic Units: The University of Leeds > Faculty of Biological Sciences (Leeds) > Institute of Molecular and Cellular Biology (Leeds)
Depositing User: Repository Officer
Date Deposited: 13 Mar 2006
Last Modified: 05 Jun 2014 19:14
Published Version: http://nar.oxfordjournals.org/cgi/reprint/33/4/139...
Status: Published
Refereed: Yes
Identification Number: 10.1093/nar/gki285
URI: http://eprints.whiterose.ac.uk/id/eprint/972

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