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.
