Sunday, September 6, 2009

The Internet ... ya gotta love it! (BioCyc.org)

The things you stumble over in the dark can be mind-bending. Take a look at BioCyc.org (http://biocyc.org/)

"Introduction to BioCyc
"The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of different organisms. The databases (DBs) within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received.
"Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating [details of Tier 1]. The BioCyc Tier 1 DBs are EcoCyc (Escherichia coli K-12) and MetaCyc (experimentally elucidated enzymes and metabolic pathways from more than 1,500 organisms.)
"Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. [details of Tier 2]
"Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 482 DBs in Tier 3. [details of Tier 3]

"Looking for pathway databases for other organisms? PGDBs have been created outside SRI for many organisms [details].
"BioCyc Tools
"Scientists can use the BioCyc Web site to visualize individual metabolic pathways, or to view the complete metabolic map of an organism [example]. The latter diagram can be used to analyze gene expression, proteomics, or metabolomics data using the Omics Viewers, such as to produce animated views of time-course gene-expression experiments [example]. The BioCyc Web site also provides genome browsing capabilities [example], and for the EcoCyc DB in particular, provides extensive information about transcriptional mechanisms of gene regulation [example]. BioCyc also provides comparative analysis tools (see Tools -> Comparative Analysis in the toolbar)"
source: http://biocyc.org/

A search for desulfurization produced the following ...

MetaCyc Pathway: dibenzothiophene desulfurization
http://biocyc.org/META/NEW-IMAGE?object=PWY-681

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