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Online Journal of Bioinformatics ©
Volume 9 (2):108-112, 2008.
CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories
Hu Zhi-Liang1, Bao J2, Reecy JM1
1Department(s) of Animal Science and 2Computer Science, Iowa State University, Ames, Iowa, USA
Zhi-Liang Hu, Bao J, Reecy JM., CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories, Onl J Bioinform., 9(2):108-112, 2008. With the accelerating rate at which gene-associated research data are accumulated, there is a growing need for batch analysis of large-scale sequence annotations such as Gene Ontology (GO). A frustrating problem with GO annotation has been the inability to properly count the occurrences of GO terms within certain parental categories under a given classification method such as GO Slim. The GO term occurrence count by category can also be time consuming when all possible paths are searched with looped structured query language (SQL). The CateGOrizer we present here is designed to overcome these problems. The CateGOrizer utilizes pre-computed transitive closure paths, performs GO classification count under any given GO slim through a web interface. Our approach has significantly reduced the run time and improved flexibility in comparison to peer programs. However, users are advised to take caution when choosing a proper classification system, to design a strategy objectively count GO terms and properly interpret the results.
Key-Words: Analysis, Gene Ontology, classifications