Novel and efficient tag SNPs selection algorithms

Bio-Medical Materials and Engineering

Volumn 24, Issue 1, 2014, Pages 1383-1389

  Chen, Wen Pei ^a   Hung, Che Lun ^a   Tsai, Suh Jen Jane ^a   Lin, Yaw Ling ^a  

^a PROVIDENCE UNIVERSITY   (Taiwan)

Author keywords

hadoop; haplotype block; non redundant site; redundant ratio; SNP; tag SNP selection

Indexed keywords

HADOOP; HAPLOTYPES; NON-REDUNDANT; REDUNDANT RATIO; SNP; TAG SNP;

BIOMEDICAL ENGINEERING; BIOTECHNOLOGY; SITE SELECTION; WEB SERVICES;

ALGORITHMS;

ALGORITHM; CHROMOSOME 20; CONFERENCE PAPER; HAPLOTYPE; HAPLOTYPE MAP; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

HADOOP; HAPLOTYPE BLOCK; NON-REDUNDANT SITE; REDUNDANT RATIO; SNP; TAG SNP SELECTION;

ALGORITHMS; CHROMOSOMES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENOTYPE; HAPLOTYPES; HUMANS; PATTERN RECOGNITION, AUTOMATED; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84891045839     PISSN: 09592989     EISSN: None     Source Type: Journal    
DOI: 10.3233/BME-130942     Document Type: Conference Paper

References (24)

1. Penelope E. Bonnen, Peggy J. Wang, Marek Kimmel, Ranajit Chakraborty, and David L. Nelson. Haplotype and linkage disequilibrium architecture for human cancer-associated genes. Genome Research, 12(12):1846-1853, 2002.
2. M. Daly, J. Rioux, S. Schafiner, T. Hudson, and E. Lander. Highresolution haplotype structure in the human genome. Nature Genetics, 29:229-232, 2001.
3. E. Dawson, G. Abecasis, et al. A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418:544- 548, 2002.
4. Jeffrey Dean and Sanjay Ghemawat. Mapreduce: A flexible data processing tool. Commun. ACM, 53(1):72-77, January 2010.
5. Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, and Xuegong Zhang. htsnper1. 0: Software for haplotype block partition and htsnps selection. BMC Bioinformatics, 6(1):38, 2005.
6. S. B. Gabriel, S. F. Schaffner, H. Nguyen, et al. The structure of haplotype blocks in the human genome. Science, 296(5576):2225-2229, 2002.
7. G. Greenspan and D. Geiger. High density linkage disequilibrium mapping using models of haplotype block variation. Bioinformatics, 20(suppl 1):i137-i144, 2004.
8. R. R. Hudson and N. L. Kaplan. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111:147-164, 1985.
9. Amit Indap, Gabor Marth, Craig Struble, Peter Tonellato, and Michael Olivier. Analysis of concordance of different haplotype block partitioning algorithms. BMC Bioinformatics, 6(1):303, 2005.
10. G. C. Johnson, L. Esposito, B. J. Barratt, et al. Haplotype tagging for the identification of common disease genes. Nat Genet. , 29(2):233 - 7, Oct 2001.
11. Hung C. L. and Hua G. J. Cloud computing for protein-ligand binding site comparison. Biomed Research International, 2013.
12. Hung C. L. and Lin Y. L. Implementation of a parallel protein structure alignment service on cloud. International Journal of Genomics, 2013.
13. Hung C. L. and Lin C. Y. Open reading frame phylogenetic analysis on the cloud. International Journal of Genomics, 2013.
14. Yaw-Ling Lin. Efficient algorithms for SNP haplotype block selection problems. In Proceedings of the 14th annual international conference on Computing and Combinatorics, COCOON '08, pages 309-318, Berlin, Heidelberg, 2008. Springer-Verlag.
15. Alfonso Mas, E. Blanco, G. Monux, E. Urcelay, F. J. Serrano, E. G. de la Concha, and A. Martinez. Drb1-tnf-tnf- haplotype is strongly associated with severe aortoiliac occlusive disease, a clinical form of atherosclerosis. Human Immunology, 66(10):1062 - 1067, 2005.
16. Petra Nowotny, Jennifer M Kwon, and Alison M Goate. SNP analysis to dissect human traits. Current Opinion in Neurobiology, 11(5):637 - 641, 2001.
17. N. Patil, A. J. Berno, D. A. Hinds, et al. Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science, 294:1719-1723, 2001.
18. A Reif, S Herterich, A Strobel, A-C Ehlis, D Saur, C P Jacob, T Wienker, T Topner, S Fritzen, U Walter, A Schmitt, A J Fallgatter, and K-P Lesch. A neuronal nitric oxide synthase NOS-I haplotype associated with schizophrenia modifies prefrontal cortex function. Mol Psychiatry, 11(3):286 - 300, 2006.
19. Michael C. Schatz. Cloudburst: Highly sensitive read mapping with mapreduce. Bioinformatics, 25(11):1363-1369, 2009.
20. Paola Sebastiani, Ross Lazarus, Scott T. Weiss, Louis M. Kunkel, Isaac S. Kohane, and Marco F. Ramoni. Minimal haplotype tagging. Proceedings of the National Academy of Sciences, 100(17):9900-9905, 2003.
21. Ronald Taylor. An overview of the hadoop/mapreduce/hbase framework and its current applications in bioinformatics. BMC Bioinformatics, 11(Suppl 12):S1, 2010.
22. N. Wang, J. M. Akey, K. Zhang, R. Chakraborty, and L. Jin. Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. Am. J. Human Genetics, 71:1227-1234, 2002.
23. J. Zahiri, G. Mahdevar, A. Nowzari-dalini, H. Ahrabian, and M. Sadeghi. A novel efficient dynamic programming algorithm for haplotype block partitioning. Journal of Theoretical Biology, 267(2):164 - 170, 2010.
24. Kui Zhang, Fengzhu Sun, Michael S. Waterman, and Ting Chen. Dynamic programming algorithms for haplotype block partitioning: Applications to human chromosome 21 haplotype data. In RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biology, pages 332-340, New York, NY, USA, 2003. ACM Press.