Metabolic reconstruction on the WWW

Natalie Maltsev maltsev at mcs.anl.gov
Sun Sep 29 12:43:53 EST 1996



Dear colleagues,

	We are glad to announce availability of WIT/PUMA2 system,
developed at Argonne National Laboratory. A system supports metabolic
reconstructions and integration of sequence, phylogenetic and
metabolic information in a coherent interactive environment. 

It consists of two parts:

    1. WIT (http://www.cme.msu.edu/WIT/)	
       WIT -- is an interactive tool for an expert biologist, which
       allows one to develop a metabolic reconstruction for an
       organism (from a complete, or partial genome).
       It supports the following steps in genome analysis:

	-- Initial assignment of functions to ORF's
	-- Development of the overview of metabolism that can be readily
	   inferred from the initial set of function alassignments. 
	-- Identification of "missing, but probably present" enzymes,
	   followed by an effort to locate candidates among the ORFs
	   that might encode  the functions. 
	-- "Balancing" the inferred metabolic components,verifying that all
	   required substrates are actually available (either produced or
	   imported), and that all products have an potential consumer. 
	-- Identification of the basic components of replication,
	   transcription, translation, DNA repair, and so forth. 
	-- Integration into a comprehensive overview of the organism with
	   function as accurately connected to sequence as possible. 

     2. PUMA

	PUMA is a repository of the metabolic models for the
        organisms, developed in WIT, on different stages of
        development.  Need to say, that Metabolic Reconstruction of
        Haemophilus influenzae, Mycoplasma genitalium and
        Saccharomyces cerevisiae are close to completion.  

We believe, that the PUMA/WIT system provides:

	1. More reliably annotated genomes due to usage of metabolic
	   reconstruction.

	2. An overview of the metabolism for an organism, connected to
	  the sequence data, data on regulatory patterns, protein
	  alignments and phylogenetic trees. 

Ross Overbeek,
Natalia Maltsev,
Niels Larsen,
Evgeni Selkov


Please, forward your questions and suggestions about usage of
the system for Metabolic Reconstruction to Ross Overbeek
overbeek at mcs.anl.gov. 





More information about the Comp-bio mailing list