PIGOK

Protein Interrogation of Gene Ontology and KEGG databases

A pigok fish

 

 

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