The PIGOK SQL database holds the pI, Molecular Weight, Codon Adaptation Index, Species, Entrez Gene number, Gene Ontology and KEGG information for each protein entry. Here are some examples of the types of graphs you can generate from the results of a search with the CAI and GO Slim Summaries.
Academic users may freely use this site and all associated information. Non-academic users are requested to obtain a license agreement for access to the Kyoto Encyclopedia of Genes and Genomes data through the licensor, Pathway Solutions Inc., as end users of a third-party program that accesses the KEGG ftp site.
There are two CGI’s that can be used to access the data:
PIGOK Lookup: |
The PIGOK lookup CGI is a front end to the PIGOK SQLdatabase. It can lookup the pI, Molecular Weight, Codon Adaptation Index ,Species, Entrez Gene number, Gene Ontology and KEGG information for each protein entry. |
PIGOK Sum: |
The PIGOK Sum CGI accepts a list of accession numbers and after removing duplicates, looks up the selected GO and KEGG pathway information which it returns as a list with all the names number of occurrences for each entries. This script was used to generate the example graphs. |
To find out more about PIGOK please see the recent publication in The Journal of Proteome Research.
PIGOK currently contains data from and links to these databases:
| Database | Source | Database release number or date |
| S. cerevisiae | Saccharomyces Genome Database |
September 26, 2006 |
| S. pombe | Schizosaccharomyces pombe GeneDB |
September 26, 2006 |
| Swissprot | Database from Swissprot Gene Ontology from EBI GOA |
50.7 |
| IPI Human | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.21 |
| IPI Rat | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.21 |
| IPI Mouse | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.21 |
| IPI Cow | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.07 |
| IPI Zebrafish | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.20 |
| IPI Chicken | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.15 |
| IPI Arabidopsis | Database from IPI Gene Ontology from GOA Gene names from Entrez Gene |
3.19 |
Links are provided to the original sources, SRS, Entrez Gene and KEGG . The pI, molecular weight and where appropriate the CAI, have been generated with the EMBOSS suite of programs and BioPerl. The database now incorporates the Gene Ontology Slim definitions.
A complete list of CAI values for S. pombe and S. cerevisiae suitable for graphing are also available.
GO Slim summaries suitable for pie charts are available for the following
databases: IPI Human, IPI Rat, IPI Mouse, Spombe.
Pigok is the local name for a perch like fish Therapon cancellatus or Mesopristes
cancellatus found in the Northern Mindanao region of the Philippines. The fish is also known by various other names e.g.Grunters or tigerperches in its habitat of the brackish waters of bays and estuaries surrounding the western pacific.
Known bugs
There are currently no known bugs. If you find one please contact me with details for a fix.
Changelog
- Project initiated June 23, 2003.
- Database loaded with spombe data. CGI working on June 24, 2003.
- Added support for swissprot on August 5, 2003.
- Added support for IPI databases on February 20, 2004.
- Lookup CGI script updated and optimized and the database was indexed for
a big speed increase on July 19, 2004. - Converted Lookup CGI to mod perl, changed SQL queries to use place settings
on September 2, 2004. - Added support for the GO slim values on May 4, 2005.
- Name changed from LookupDB to PIGOK on May 20th, 2005.
- KEGG data imported into PIGOK database and the Lookup CGI was edited to
access the data locally rather than remotely resulting in faster response
times on September 14, 2005. - Excel file export added, protein name and www link columns added, improved
selection options for GO Slim definitions, duplicate accession number
bug fixed for the Lookup CGI on October 23, 2005. - Added the Sum CGI. Edited the main html page and the individual html pages
for the two CGI’s on October 25, 2005. - Minor changes to database processing and loading scripts on Sunday 1st October 2006.