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:: PUMA2 ::
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High throughput comparative and evolutionary
analysis of genomes and metabolic networks with Grid
computational backend.
PUMA2 contains over 1,000 Prokaryotic
and Eukaryotic genomes, and allows interactive analysis of the sequence data using a
variety of bioinformatics tools.
Please cite:
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D'Souza M.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D369-72.
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:: Announcements ::
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 View the latest GNARE newsletter.
GNARE (GeNome Analysis and Research Environment) is a bioinformatics server that supports both automated and interactive analysis of
user-submitted genomes and metagenomes. It allows
scientific groups and individual users to analyze genomic data using an
integrated and automated bioinformatics environment based on advanced
computational technologies and Grid resources.
Submit your genome to GNARE! (Don't forget to register first)
View sample user genomes analyzed by GNARE, no registration required.
We are pleased to announce the completion of a successful user genome annotation workshop using GNARE! Access the online tutorial here.
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Explore PUMA2 ...
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Organism Models
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Explore genomic context of a particular organism
or
Perform searches in sets of organisms
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Functional Overview
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Browse Metabolic Reconstruction from
EMP database
Browse Metabolic Reconstruction from
KEGG database
Browse Reconstruction of KEGG
two component signal transduction system
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PUMA2 tools
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We have developed tools for high-resolution analysis of Protein families:
Chisel -- an algorithm and a
library for annotation and identification of evolutionary versions of enzymes
PhyloBlocks -- identification
of conserved domains and motifs using Blocks in a context of a phylogenetic tree
BloBlast -- PhyloBlocks enchanced Blast
SVMMER -- SVM-based protein identification
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:: Registration ::
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You need to register to add your annotations or develop your own models in PUMA2
Non-registered users can browse PUMA2 and perform interactive analysis of the data.
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:: New features in current release ::
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Comparative analysis using phenotypic data is now available.
Metabolic reconstructions using two data sources EMP and KEGG for all complete publicly available genomes!
Interactive analysis of the data by variety of bioinformatics tools.
Supports user annotations and functional assignments.
Precomputed sequence analysis results using GADU/Gnare Grid server.
Provides access to metabolic pathways from the EMP database.
Please direct your comments, suggestions and bug reports to puma2@mcs.anl.gov.
Submit your genome to GNARE.
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:: Next release ::
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Alternative metabolic reconstructions using KEGG maps.
Build your own pathways.
PUMA2 and Chisel function predictions for public genomes will be available.
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