Bioinformatics Group at MCS ANL Projects
High throughput comparative and evolutionary analysis of Genomes and metabolic networks with Grid computational backend
PUMA2 -- a system for High-throughput analysis of genomes and metabolic reconstructions from the sequence data. Currently PUMA2 contains 1034 genomes and allows interactive analysis of the sequence data using a variety of bioinformatics tools.
The beta version of PUMA2 was released in September 2004.
GADU -- an automated Genome Analysis and Database Update server with Grid technology-based computational backend
Tools and Databases for Evolutionary Analysis of Gene Networks and their components
We are developing tools and curated databases for high-resolution evolutionary analysis of proteins families, prediction of the protein function and exploration of the implementations of the same function in various taxonomic and phenotypic groups of the organisms.
Tools:
- Chisel -- high resolution tool for automated identification of evolutionary versions of enzymatic functions.
- PhyloBlocks -- an interactive tool for evolutionary analysis of protein families >> more information
- SVMMER (in collaboration with ORNL) -- support vector machine-base tool for functional analysis and classification of proteins more information
- BloBla -- PhyloBlocks enriched Blast
Databases:
- Sentra -- a database of prokaryotic Signal Transduction proteins >> more information
- SubUnits -- a database of Enzymatic subunits
- Pathos -- a database supporting the NIH Center of Excellence in Biodefense research
- TarGet -- a database supporting the NIH Midwest Structural Biology Center >> more information
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