1. BioCarta
Main focus: Pathways and tools to study them.
Pathway tool is web-based. http://www.biocarta.com/genes/index.asp
Static pages of pathways. Metabolic and regulatory pathways.
Need licence to add/edit pathways.
1.2 BioCarta Metabolic Pathway Example Glycolysis. Compounds
shown in chemical and textual form.
Enzymes above arrows with legend at bottom.
Only enzymes are clickable.
2. ExPASy “Expert Protein Analysis System”. Main focus: Analysis of protein sequences and
structures. Pathway tool is web-based.
http://www.expasy.org/cgi-bin/search-biochem-index
Static pages of pathways. Metabolic and Regulatory pathways. Scanned in version of the Boehringer Mannheim
“Biochemical Pathways” map. Map partitioned into 115 pieces. Keywords matched against entries in map.
Cannot add/edit pathways.
2.2 ExPASy Metabolic Pathway Example Glycolysis. Color convention
based on Michal’s “Biochemical Pathways”.
Color of compounds depends on compound type.
Color of arrows depend on species (plant, animal, yeast, prokaryotes).
Only enzymes and arrows outside diagram are clickable.
2.3 ExPASy Regulatory Pathway Example Insulin receptors. Only enzymes
and arrows outside diagram are clickable.
3. KEGG “Kyoto Encyclopedia of Genes and
Genomes”. Main focus: Biochemical pathway
visualization. Pathway tool is web-based.
http://www.kegg.com/kegg/kegg2.html Static pages of pathways.
Metabolic and Regulatory pathways. Different organisms.
3.2 KEGG Metabolic Pathway Example
Glycolysis. Substrates and
products are drawn in circles.
Enzymes, represented by EC number, are drawn in rectangles.
Adjacent pathways are drawn in semi-rectangles.
Enzymes found in the gene catalog of a specific organism are marked green.
All items are clickable.
4. WIT “What is There”. Main focus: Produce metabolic
reconstructions for sequenced (or partially sequenced) genomes.
Pathway tool is Web-based.http://wit.mcs.anl.gov/WIT2/
Static pages of pathways. Only metabolic pathways.
5. MetaCyc Electronic encyclopedia of over 450 metabolic
pathways from over 150 different organisms. Software:
Implemented in COMMON LISP; AI techniques incorporated to allow inference, such as pathway prediction from sequenced genomes.
Need a licence to obtain software. Free for academic purposes only.
Graph layout algorithm for drawing metabolic pathways dynamically at run-time.
Need to manipulate database to add/edit pathways.