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. 2006 Jan 1;34(Database issue):D369-72.
doi: 10.1093/nar/gkj095.

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

Natalia Maltsev  1 , Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H Syed, Tanuja Bompada, Yi Zhang, Mark D'Souza
Affiliations

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

Natalia Maltsev et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Representation of the stages of analyses of genomes in PUMA2. Users can browse data that is integrated and analyzed in PUMA2 or submit their own sequences. Precomputed results for homology, domain architecture, functional analysis and metabolic reconstructions are provided in an interactive framework.
See this image and copyright information in PMC

References

    1. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32:D277–D280. - PMC - PubMed
    1. Krieger C.J., Zhang P., Mueller L.A., Wang A., Paley S., Arnaud M., Pick J., Rhee S.Y., Karp P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004;32:D438–D442. - PMC - PubMed
    1. Markowitz V., Korzeniewski F., Palaniappan K., Szeto E., Werner G., Padki A., Zhao X., Dubchak I., Hugenholtz P., Anderson I., et al. The Integrated Microbial Genomes (IMG) System. Nucleic Acids Res. 2006 in press. - PMC - PubMed
    1. Overbeek R., Larsen N., Pusch G.D., D'Souza M., Selkov E., Jr, , Kyrpides N., Fonstein M., Maltsev N., Selkov E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 2000;28:123–125. - PMC - PubMed
    1. Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Church D.M., DiCuccio M., Edgar R., Federhen S., Helmberg W., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2005;33:D39–D45. - PMC - PubMed

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