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Nucleic Acids Research 2006 34(Database Issue):D369-D372; doi:10.1093/nar/gkj095
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Nucleic Acids Research, 2006, Vol. 34, Database issue D369-D372
© The Author 2006. 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}oxfordjournals.org

Article

PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways

Natalia Maltsev1,2,*, Elizabeth Glass1,2, Dinanath Sulakhe1, Alexis Rodriguez1, Mustafa H. Syed1, Tanuja Bompada1, Yi Zhang3 and Mark D'Souza2

1Mathematics and Computer Science Division, Argonne National Laboratory Argonne, IL 60439, USA 2Computation Institute, University of Chicago Chicago, IL 60637, USA 3University of Illinois at Chicago Chicago, IL 60607, USA

*To whom correspondence should be addressed: Tel: +1 630 252 5195; Fax: +1 630 252 5986; Email: maltsev{at}mcs.anl.gov

Received August 15, 2005. Revised October 16, 2005. Accepted October 16, 2005.

The PUMA2 system (available at http://compbio.mcs.anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. PUMA2 provides a framework for comparative and evolutionary analysis of genomic data and metabolic networks in the context of taxonomic and phenotypic information. Grid infrastructure is used to perform computationally intensive tasks. PUMA2 currently contains precomputed analysis of 213 prokaryotic, 22 eukaryotic, 650 mitochondrial and 1493 viral genomes and automated metabolic reconstructions for >200 organisms. Genomic data is annotated with information integrated from >20 sequence, structural and metabolic databases and ontologies. PUMA2 supports both automated and interactive expert-driven annotation of genomes, using a variety of publicly available bioinformatics tools. It also contains a suite of unique PUMA2 tools for automated assignment of gene function, evolutionary analysis of protein families and comparative analysis of metabolic pathways. PUMA2 allows users to submit batch sequence data for automated functional analysis and construction of metabolic models. The results of these analyses are made available to the users in the PUMA2 environment for further interactive sequence analysis and annotation.

Correspondence may also be addressed to Mark D'Souza. Tel: +1 630 252 7137; Fax: +1 630 252 5986; Email: dsouza{at}mcs.anl.gov


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