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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Livestock Issues Research » Research » Publications at this Location » Publication #171404
Title: HIGH THROUGHPUT GENE ONTOLOGY FUNCTIONAL ANNOTATION TOOLKIT (HT-GO-FAT) UTILIZED FOR ANIMAL AND PLANT

Author
item Dowd, Scot
item Zaragoza, Joaquin

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2004
Publication Date: 1/15/2005
Citation: Dowd, S.E., Zaragoza, J. 2005. High throughput gene ontology functional annotation toolkit (HT-GO-FAT) utilized for animal and plant [abstract]. Plant and Animal Genome Conference, January 15-19, 2005. Available: http://www.intl-pag.org/13/abstracts/PAG13_P724.html

Interpretive Summary:

Technical Abstract: With the growing popularity of functional genomics and the usefulness of visualization and functional classification schemes such as Gene Ontology (GO), Enzyme Commission numbers (EC), BioCarta Pathways, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, there is a need to make them more accessible to a growing number of geneticists and molecular biologists. HT-GO-FAT is a comprehensive software toolkit that can generate, encapsulate, and present this data in a manageable and user friendly way. HT-GO-FAT was developed using C# and the Windows .NET framework. The application utilizes a custom curated BLAST database that is updated monthly (downloadable) as well as custom designed mySQL relational database that is also updated monthly. HT-GO-FAT provides the scientist with comprehensive user interface to query sequences against the databases associations and view the results in a tabular format. The associations generated by HT-GO-FAT in turn automatically generate specific molecular and cellular pathway images displaying the significant genes selected from the BLAST output. To further aid in annotation, the software can export data files directly used to create customized AMIGO databases, submit to GenBank, or simply import to other databases for further analyses. This toolkit has been successfully utilized to curate and annotate various EST plant data sets including Cotton, Tortula ruralis, and Physcomitrella patens and was recently utilized to perform functional annotation of a wide range of NCBI unigene sets including pig, cow, and chicken.