WIT2 |
WIT2
-- an integrated system for support of genetic sequence and
comparative analysis of sequenced genomes, it also supports, metabolic reconstructions
from the sequence data.
WIT2 now contains data from 38 completely and almost completely sequenced
genomes. WIT2 provides access to thoroughly annotated genomes within a
framework of metabolic reconstructions, connected to the sequence data;
protein alignments and phylogenetic trees and data on gene clusters,
potential operons and functional domains. |
|
EMP
|
EMP
, the largest publicly available database of Enzymes and Metabolic
Pathways in the world. It represents a collaborative effort between
Argonne National Laboratory and The Institute of Theoretical Biophysics
(Russian Academy of Sciences, Puschino, Russia), led by Prof. E. Selkov.
It represents a key resource for developing detailed metabolic
reconstructions for newly sequenced genomes far more rapidly than researchers
even a few years ago would have thought possible. EMP/MPW database currently
contains 28, 100 records, which encode the full factual content of 17, 500 publications
describing more than 8, 000 organisms. The database contains information
on 3, 900 enzymes, including data on enzyme specificity, enzymological constants,
purification protocols, regulation, inhibitors and activators. |
|
MPW
|
MPW
, Prof. Selkov's collection of
metabolic and functional diagrams. The MPW collection contains
more then 3, 000 metabolic and functional diagrams representing functionality
in 211 different organisms. |
PUMA2
(a prototype)
|
 PUMA2
, an environment for comparative analysis
of metabolic subsystems automated reconstruction of metabolism
of microbial consortia, and individual organisms from sequence
data
Analyses in PUMA2 will be based on a collection of metabolic modules
connected to sequence data. The results of such analyses will be presented
in graphical form based on hierarchical representation of the functional
subsystems and annotated with sequence data and literature information. |
|
SENTRA
|
SENTRA
, a database of sensory signal transduction
proteins,
includes information about sensory transduction proteins in 38 WIT genomes,
as well as annotated data from the SwissProt and EMBL databases. |
|
Other databases
|
A
Database of Translation-Associated Proteins This
project involves analysis of all translation factors in complete archaeal
genomes.
A
Database of Transcription-Associated Proteins This
project involves analysis of all transcription factors in complete archaeal
genomes. These
projects were carried out by Dr. Nikos Kyrpides in collaboration with UIUC.
Database
of Phenotypes -- We have started developing a database
of phenotypic data for the sequenced genomes . We believe that availability
of phenotypic data will enhance annotation of the genomes and will aid in
the curation and development of metabolic reconstructions in PUMA |
|
|
PatScan
-- is a publicly-accessible web-application which enables users to search
for patterns in nucleotide and protein sequences. User-defined patterns,
(e.g. potential stem-loop structures in nucleotide sequences, or motifs
in protein sequences) could be searched against the protein sequence databases
such as SWISS-PROT, TrEMBL, PDB, as well as EMBL nucleotide sequence database. |
