Knowledge Discovery in GENBANK

Wedescribe various methods designed to discover knowledge in the GenBanknucleic acid sequence database. Using a grammatical model of gene structure, we create a parse tree of a gene using features listed in the FEATURETABLE. Theparse tree infers features that are not explicitly listed, but which follow from the listed features. This method discovers 30%more introns and 40% more exons when applied to a globin gene subset of GenBank. Parse tree construction also entails resolving ambiguity and inconsistency within a FEATURETABLE.We transform the parse tree into an augmented FEATURETABLEthat represents inferred gene structure explicitly and unambiguously, thereby greatly improving the utility of the FEATURETABLEto researchers. Wethen describe various analogical reasoning techniques designed to exploit the homologous nature of genes. Webuild a classification hierarchy that reflects the evolutionary relationship between genes. Descriptive grammars of gene classes are then induced from the ...

• Type: Conference
• Year: 1993
• Where: ISMB
• Authors: Jeffery S. Aaronson, Juergen Haas, G. Christian Overton
• Keywords: Computational Biology, Gene, Globin Gene Subset, ISMB 1993, Parse Tree