Skip Navigation

Nucleic Acids Research 2005 33(4):1399-1409; doi:10.1093/nar/gki285
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1224K) Freely available
Right arrow Screen PDF (418K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (28)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Pinney, J. W.
Right arrow Articles by Westhead, D. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pinney, J. W.
Right arrow Articles by Westhead, D. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 3 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

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

John W. Pinney*, Martin W. Shirley1, Glenn A. McConkey and David R. Westhead

Faculty of Biological Sciences, University of Leeds LS2 9JT, UK 1Institute of Animal Health Compton, RG20 7NN, UK

*To whom correspondence should be addressed. Tel: +44 113 233 3072; Fax: +44 113 343 3167; Email: john{at}bioinformatics.leeds.ac.uk

Received January 21, 2005. Revised February 17, 2005. Accepted February 17, 2005.

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 0.5x 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. W. Whitaker, I. Letunic, G. A. McConkey, and D. R. Westhead
metaTIGER: a metabolic evolution resource
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D531 - D538.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
B. Sidders, C. Pirson, P. J. Hogarth, R. G. Hewinson, N. G. Stoker, H. M. Vordermeier, and K. Ewer
Screening of Highly Expressed Mycobacterial Genes Identifies Rv3615c as a Useful Differential Diagnostic Antigen for the Mycobacterium tuberculosis Complex
Infect. Immun., September 1, 2008; 76(9): 3932 - 3939.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Klammer, S. Roopra, and E. L. L. Sonnhammer
jSquid: a Java applet for graphical on-line network exploration
Bioinformatics, June 15, 2008; 24(12): 1467 - 1468.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Choi, R. Munch, S. Leupold, J. Klein, I. Siegel, B. Thielen, B. Benkert, M. Kucklick, M. Schobert, J. Barthelmes, et al.
SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D533 - D537.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Hyland, J. W. Pinney, G. A. McConkey, and D. R. Westhead
metaSHARK: a WWW platform for interactive exploration of metabolic networks.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W725 - W728.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. D. Hooper and P. Bork
Medusa: a simple tool for interaction graph analysis
Bioinformatics, December 15, 2005; 21(24): 4432 - 4433.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.