Index of /download/pathways

Icon  Name                    Last modified      Size  Description
[PARENTDIR] Parent Directory                             -   
[   ] calbi.tar.gz            2023-06-29 09:53   22M  
[   ] calbibase.ocelot.gz     2023-06-29 09:53  1.2M  
[   ] pathwaysAndGenes.tab    2023-06-29 09:53   22K  


The download/pathways/ directory contains metabolic pathway
information.

The pathways were created at CGD using the Pathway Tools software,
which is developed and maintained by the Bioinformatics Research Group
at SRI International (see
http://bioinformatics.ai.sri.com/ptools/). The pathway predictions are
being manually reviewed and curated at CGD, as described in more
detail on our Pathways Help page
(http://www.candidagenome.org/help/BiochemPathwaysHelp.shtml).

The genes from C. albicans SC5314 were used as input by the prediction software, 
but the manually curated pathway descriptions consider the pathway within the
broader context of metabolism within Candida species in general. 

---------------------------

pathwaysAndGenes.tab

This tab-delimited file contains a list of the metabolic pathways in
CGD, with lists of the genes that encode the enzymes within each
pathway.

Columns:

1.  UNIQUE-ID; the unique identifier (also called the "frame name") of
    the pathway
2.  NAME; the common name of the pathway
3.  GENE-NAMES; colon-delimited list of CGD standard names of the genes
    that encode the enzymes within the pathway
4.  GENE-IDS; colon-delimited list of the systematic names (orf19
    names) of the genes that encode the enzymes within the pathway

This file is updated weekly.

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calbibase.ocelot.gz

This file contains the CGD metabolic pathway information in the format
that is read by the Pathway Tools software from SRI. Information about
copying pathway databases in this format is available at:
http://bioinformatics.ai.sri.com/ptools/copy-patho-db.html

The file is gzip compressed. There are several freely available
software options for decompressing gzipped files using Windows.  The
software and other useful information is available on these web sites:
- WinZip (http://www.winzip.com/)
- Stuffit (http://www.stuffit.com/)
- Gzip (http://www.gzip.org/
   
and the gzip user's manual:
http://www.math.utah.edu/docs/info/gzip_toc.html

---------------------------

URL: www.candidagenome.org
Contact: http://www.candidagenome.org/cgi-bin/suggestion
Funding: NIDCR at US NIH, grant number 1-R01-DE015873-01