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

The PUMA2 system (available at http://compbio.mcs. 10 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 geno15 mic 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 mito20 chondrial 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 25 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 fun...

• Type: Journal
• Year: 2006
• Where: NAR
• Authors: Natalia Maltsev, Elizabeth M. Glass, Dinanath Sulakhe, Alexis A. Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang 0002, Mark D'Souza
• Keywords: Analysis, Metabolic, Metabolic Reconstructions, NAR 2006