Solving the Problem of Trans-Genomic Query with Alignment Tables

Abstract-- The trans-genomic query (TGQ) problem -- enabling the free query of biological information, even across genomes -- is a central challenge facing bioinformatics. Solutions to this problem can alter the nature of the field, moving it beyond the jungle of data integration and expanding the number and scope of questions that can be answered. An alignment table is a binary relationship on locations (sequence segments). An important special case of alignment tables are hit tables -- tables of pairs of highly similar segments produced by alignment tools like BLAST. However, alignment tables also include general binary relationships, and can represent any useful connection between sequence locations. They can be curated, and provide a high-quality queryable backbone of connections between biological information. Alignment tables thus can be a natural foundation for TGQ, as they permit a central part of the TGQ problem to be reduced to purely technical problems involving tables of lo...

• Type: Journal
• Year: 2008
• Where: TCBB
• Authors: Douglas Stott Parker Jr., Ruey-Lung Hsiao, Yi Xing, Alissa M. Resch, Christopher J. Lee
• Keywords: Alignment Tables, Binary Relationships, TCBB 2008, Trans-genomic Query