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Nucleic Acids Research, 2000, Vol. 28, No. 1 123-125
© 2000 Oxford University Press

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

Ross Overbeek1,*, Niels Larsen1, Gordon D. Pusch1, Mark D’Souza1,2, Evgeni Selkov Jr1,2, Nikos Kyrpides1, Michael Fonstein1, Natalia Maltsev2 and Evgeni Selkov1,2

1Integrated Genomics Inc., 2201 W. Campbell Park Drive, Chicago, IL 60612, USA and 2Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA

The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases. This system contains data derived from about 40 completed or nearly completed genomes. Sequence homologies, various ORF-clustering algorithms, relative gene positions on the chromosome and placement of gene products in metabolic pathways (metabolic reconstruction) can be used for the assignment of gene functions and for development of overviews of genomes within WIT. The integration of a large number of phylogenetically diverse genomes in WIT facilitates the understanding of the physiology of different organisms.

* To whom correspondence should be addressed. Tel: +1 312 491 0846; Fax: +1 312 491 0856; Email: ross@integratedgenomics.com


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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text]

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[Abstract] [Full Text]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text]

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[Abstract] [Full Text] [PDF]

Home page
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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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