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Presentation
Indexing Genomic Databases
Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering
  • Gina Cooper, Wright State University - Main Campus
  • Michael L. Raymer, Wright State University - Main Campus
  • Travis E. Doom, Wright State University - Main Campus
  • Dan E. Krane, Wright State University - Main Campus
  • Natsuhiko Futamura, Wright State University - Main Campus
Document Type
Conference Proceeding
Publication Date
5-1-2004
Abstract
Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.
Comments

Presented at the Fourth IEEE Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan, May 19-21, 2004.

Posted with permission from IEEE.

DOI
10.1109/BIBE.2004.1317395
Citation Information
Gina Cooper, Michael L. Raymer, Travis E. Doom, Dan E. Krane, et al.. "Indexing Genomic Databases" Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering (2004) p. 587 - 591 ISSN: 0769521738
Available at: http://works.bepress.com/michael_raymer/20/