Accelerating gene context analysis using bitmaps

ACM International Conference Proceeding Series

Volumn , Issue , 2013, Pages

  Romosan, Alex ^a   Shoshani, Arie ^a   Wu, Kesheng ^a   Markowitz, Victor ^a   Mavrommatis, Kostas ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BITMAP REPRESENTATION; CO-OCCURRENCE; COMPLEX QUERIES; CONTEXT ANALYSIS; GENE CASSETTES; GENE CLUSTERS; MICROBIAL GENOMES; RELATIONAL DATABASE;

INFORMATION MANAGEMENT; MANAGEMENT INFORMATION SYSTEMS; QUERY PROCESSING;

GENES;

EID: 84882974883     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2484838.2484856     Document Type: Conference Paper

References (12)

1. P. M. Bowers, M. Pellegrini, M. J. Thompson, J. Fierro, T. O. Yeates, D. Eisenberg, et al. Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol, 5(5):R35, 2004.
2. R. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, and et al. The pfam protein families database. Nucleic Acids Research, 38:D211-D222, January 2010.
3. S. Helmer and G. Moerkotte. A performance study of four index structures for set-valued attributes of low cardinality. The VLDB Journal, 12(3):244-261, 2003.
4. N. Mamoulis. Efficient processing of joins on set-valued attributes. In SIGMOD, pages 157-168. ACM, 2003.
5. V. Markowitz, I. Chen, K. Palaniappan, K. Chu, E. Szeto, and et al. Img: The integrated microbial genomes database and comparative analysis system. Nucleic Acids Res., 40:D115-D122, 2012. See also http://img.jgi.doe.gov/.
6. K. Mavromatis, K. Chu, N. Ivanova, S. Hooper, V. Markowitz, and N. Kyrpides. Gene context analysis in the integrated microbial genomes (IMG) data management system. PLoS ONE, 4(11):e7979, 2009.
7. R. Overbeek, M. Fonstein, M. D'Souza, G. Pusch, and N. Maltsev. The use of gene clusters to infer functional coupling. PNAS, 96(6):2896-901, 2009.
8. R. Tatusov, N. Fedorova, J. Jackson, A. Jacobs, B. Kiryutin, and et al. The cog database: an updated version includes eukaryotes. BMC Bioinformatics, 4:41, 2003.
9. K. Wu, E. Otoo, and A. Shoshani. On the performance of bitmap indices for high cardinality attributes. In On the Performance of Bitmap Indices for High Cardinality Attributes, pages 24-35, 2004.
10. K. Wu, E. Otoo, and A. Shoshani. Optimizing bitmap indices with efficient compression. ACM Transactions on Database Systems, 31:1-38, 2006.
11. K. Wu, A. Shoshani, and K. Stockinger. Analyses of multi-level and multi-component compressed bitmap indexes. ACM TODS, 35, 2010.
12. K. Wu, K. Stockinger, and A. Shoshani. Breaking the curse of cardinality on bitmap indexes. In Statistical and Scientific Database Management - SSDBM, pages 348-365, 2008.