HT-GO-FAT

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. 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.