An efficient two-phase algorithm to find gene-specific probes for large genomes

Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007

Volumn , Issue , 2007, Pages 205-210

  Kang, Seung Ho ^a   Choi, Mun Ho ^a   Jeong, In Seon ^a   Lim, Hyeong Seok ^a  

^a Chonnam National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; INFORMATION TECHNOLOGY; MICROARRAYS; NUCLEIC ACIDS; ORGANIC ACIDS; TECHNOLOGY; TWO PHASE FLOW;

CROSS-HYBRIDIZATION; DNA MICRO ARRAYS; FILTERING ALGORITHMS; GENE-SPECIFIC PROBES; PRE-PROCESSING ALGORITHMS; PROBE CANDIDATES; S. CEREVISIAE; SECOND PHASE; SUB-STRINGS; TIME-CONSUMING TASKS; TWO PHASE ALGORITHMS;

BIOASSAY;

EID: 49349085872     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FBIT.2007.129     Document Type: Conference Paper

References (9)

1. L. Gasieniec, C. Y. Li, P. Sant, and P. W. H. Wong, "Efficient Probe Selection in Microarray Design", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2006.
2. L. Kaderali and A. Schliep, "Selecting signature oligonucleotides to identify organisms using DNA arrays", Bioinformatics, 2002, vol. 18, no. 10, pp. 1340-1349.
3. L. Li and G. Stormo, "Selection of optimal DNA oligos for gene expression analysis", Bioinformatics, 2001, vol. 17, no. 11, pp. 1067-1076.
4. D. J. Lockhart, H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S.Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown, "Expression monitoring by hybridization to high-density oligonucleotide arrays", Nature Biotechnology, 1996, vol. 14, pp. 1675-1680.
5. D. W. Mount, Bioinformatics Sequence and Genome Analysis (2nd ed), CSHLPress, 2004.
6. S. Rahmann, "Rapid large-scale oligonucleotide selection for microarrays", Proc. IEEE Computer Society Bioinformatics Conference, 2002, vol. 1, pp. 54-63.
7. S. Rahmann, "Fast and sensitive probe selection for DNA chips using jumps in matching statistics", Proc. IEEE Computational Systems Bioinformatics, 2003, vol. 2, pp. 57-64.
8. J. J. SantaLucia, H. T. Allawi, and P. A. Seneviratne, "Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability", Biochemistry, 1996, vol. 35, pp, 3555-3562.
9. W. Sung and W. Lee, "Fast and accurate probe selection algorithm for large genomes", Proc. IEEE Computational Systems Bioinformatics, 2003, vol. 2, pp. 65-74.