title: PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.
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.
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA. maltsev@mcs.anl.gov
authors.forename: Natalia
authors.initials: N
authors.lastname: Maltsev
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Glass
authors.forename: Dinanath
authors.initials: D
authors.lastname: Sulakhe
authors.forename: Alexis
authors.initials: A
authors.lastname: Rodriguez
authors.forename: Mustafa H
authors.initials: MH
authors.lastname: Syed
authors.forename: Tanuja
authors.initials: T
authors.lastname: Bompada
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Mark
authors.initials: M
authors.lastname: D'Souza
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D004798:Enzymes / Q000737:chemistry; D019143:Evolution, Molecular; D023281:Genomics; D020407:Internet; D008660:Metabolism / Q000235:genetics*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D004798:Enzymes