PIGOK

Protein Interrogation of Gene Ontology and KEGG databases

This cgi is a front end to the PIGOK SQL database. The database holds the pI, Molecular Weight, Codon Adaptation Index ,Species, Entrez Gene number and Gene Ontology information for each protein entry. The cgi also generates links to the KEGG database or can query it directly and determine and report links to the actual KEGG pathways. Here are some examples of the types of graphs you can generate from the results of a search and the CAI and GO Slim Summaries.

Enter a list of accession numbers that you wish to view.

Accession Numbers
	For example: SPBP8B7.05c SPAC11E3.07 SPAC14C4.14 SPAC16E8.07c SPAC17A2.03c SPAC1B3.14 SPAC222.12c SPAC23C4.11 SPAC2C4.13 SPAC343.05 SPAC637.05c SPAC732.01 P33412 Q9ZBY8 P50502 Q02318 P74892 O05643 Q97G69 IPI00220665 IPI00008527 IPI00010418 IPI00303158 IPI00297532

Select the values you wish reported:

pI	Molecular Weight	Codon Adaptation Index	Species	KEGG	GO numbers and descriptions	GO slim values

PIGOK currently contains links to these databases:

Database	Source	Number of entries	Number of Gene Ontology entries	Date updated
S. cerevisiae	Saccharomyces Genome Database	6274	13875	28/07/2003
S. pombe	Schizosaccharomyces pombe GeneDB	5021	18958	19/05/2005
Swissprot	Database from Swissprot Gene Ontology from EBI GOA	153871	1001242	19/05/2005
IPI Rat	Database from IPI Gene Ontology from GOA Gene names from Rat Genome Database	39374	61620	19/05/2005
IPI Human	Database from IPI Gene Ontology from GOA Gene names from Entrez Gene	49923	113218	19/05/2005
IPI Mouse	Database from IPI Gene Ontology from GOA Gene names from Entrez Gene	42801	107669	19/05/2005

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 English translation of the Chinese name for a perch like fish Therapon cancellatus.
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

Unfortunately there is still a bug in the CGI when duplicate accession numbers are submitted the CGI returns erroneous line in the table with repeated GO information. This bug will be fixed as soon as possible. The work around is to remove duplicate entries from the list. May 22, 2005.

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.
CGI script updated and optimized and the database was indexed for a big speed increase on July 19, 2004.
Converted 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 CGI was edited to access the data localy rather than remotely resulting in faster response times on September 14, 2005.

Contact Richard Jacob if you have questions or bug reports.

Last updated September 14, 2005