Bioinformatics Vol. 19 no. 10 2003
Pages 1300-1301
© 2003 Oxford University Press
Applications Note |
HaploBlockFinder: haplotype block analyses
Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
Received on September 16, 2002
; revised on November 17, 2002
; accepted on January 25, 2003
Summary: Recent studies have unveiled discrete block-like structures of linkage disequilibrium (LD) in the human genome. We have developed a set of computer programs to analyze the block-like LD structures (haplotype blocks) based on haplotype data. Three definitions of haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage. Tagged SNPs that uniquely distinguish common haplotypes are identified. A greedy algorithm was used to improve the efficiency. Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium.
Availability: A web interface for the HaploBlockFinder is available at http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi the source codes are also freely available on the web site.
Contact: jinl{at}ucmail.uc.edu
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H Li, N L-S Tang, P K-S Chan, C-Y Wang, D S-C Hui, C Luk, R Kwok, W Huang, J J-Y Sung, Q-P Kong, et al. Polymorphisms in the C-type lectin genes cluster in chromosome 19 and predisposition to severe acute respiratory syndrome coronavirus (SARS-CoV) infection J. Med. Genet., November 1, 2008; 45(11): 752 - 758. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Wiedmann, M. Fischer, M. Koehler, K. Neureuther, G. Riegger, A. Doering, H. Schunkert, C. Hengstenberg, and A. Baessler Genetic Variants Within the LPIN1 Gene, Encoding Lipin, Are Influencing Phenotypes of the Metabolic Syndrome in Humans Diabetes, January 1, 2008; 57(1): 209 - 217. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. L. Hong, D. Huo, H.-J. Kim, Q. Niu, D. L. Fackenthal, S. A. Cummings, E. M. John, D. W. West, A. S. Whittemore, S. Das, et al. UDP-Glucuronosyltransferase 1A1 Gene Polymorphisms and Total Bilirubin Levels in an Ethnically Diverse Cohort of Women Drug Metab. Dispos., August 1, 2007; 35(8): 1254 - 1261. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Krynetskiy and P. McDonnell Building Individualized Medicine: Prevention of Adverse Reactions to Warfarin Therapy J. Pharmacol. Exp. Ther., August 1, 2007; 322(2): 427 - 434. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Khatkar, K. R. Zenger, M. Hobbs, R. J. Hawken, J. A. L. Cavanagh, W. Barris, A. E. McClintock, S. McClintock, P. C. Thomson, B. Tier, et al. A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein-Friesian Cattle Genetics, June 1, 2007; 176(2): 763 - 772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Butty, M. Roy, P. Sabeti, W. Besse, C. Benoist, and D. Mathis Signatures of strong population differentiation shape extended haplotypes across the human CD28, CTLA4, and ICOS costimulatory genes PNAS, January 9, 2007; 104(2): 570 - 575. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M J Bugeja, D R Booth, B H Bennetts, R N. Heard, and G J Stewart An investigation of polymorphisms in the 4q13.3-21.1 CXC chemokine gene cluster for association with multiple sclerosis in Australians Multiple Sclerosis, November 1, 2006; 12(6): 710 - 722. [Abstract] [PDF]
|
|
|
|
|
|
G. Greenspan and D. Geiger Modeling Haplotype Block Variation Using Markov Chains Genetics, April 1, 2006; 172(4): 2583 - 2599. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. C. Gonzalez-Martinez, E. Ersoz, G. R. Brown, N. C. Wheeler, and D. B. Neale DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L. Genetics, March 1, 2006; 172(3): 1915 - 1926. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. S. Qin, S. Gopalakrishnan, and G. R. Abecasis An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria Bioinformatics, January 15, 2006; 22(2): 220 - 225. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. V. Krutovsky and D. B. Neale Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir Genetics, December 1, 2005; 171(4): 2029 - 2041. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Takeuchi, K. Yanai, T. Morii, Y. Ishinaga, K. Taniguchi-Yanai, S. Nagano, and N. Kato Linkage Disequilibrium Grouping of Single Nucleotide Polymorphisms (SNPs) Reflecting Haplotype Phylogeny for Efficient Selection of Tag SNPs Genetics, May 1, 2005; 170(1): 291 - 304. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. F. Verhoeven and K. L. Simonsen Genomic Haplotype Blocks May Not Accurately Reflect Spatial Variation in Historic Recombination Intensity Mol. Biol. Evol., March 1, 2005; 22(3): 735 - 740. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Zhang, Z. Qin, T. Chen, J. S. Liu, M. S. Waterman, and F. Sun HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms Bioinformatics, January 1, 2005; 21(1): 131 - 134. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. R. Linder and L. H. Rieseberg Reconstructing patterns of reticulate evolution in plants. Am. J. Botany, October 1, 2004; 91: 1700 - 1708. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Q.-f. Wang, X. Liu, J. O'Connell, Z. Peng, R. M. Krauss, D. L. Rainwater, J. L. VandeBerg, Edward. M. Rubin, J.-F. Cheng, and L. A. Pennacchio Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons Hum. Mol. Genet., May 15, 2004; 13(10): 1049 - 1056. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. D. Love-Gregory, J. Wasson, J. Ma, C. H. Jin, B. Glaser, B. K. Suarez, and M. A. Permutt A Common Polymorphism in the Upstream Promoter Region of the Hepatocyte Nuclear Factor-4{alpha} Gene on Chromosome 20q Is Associated With Type 2 Diabetes and Appears to Contribute to the Evidence for Linkage in an Ashkenazi Jewish Population Diabetes, April 1, 2004; 53(4): 1134 - 1140. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. G. Schulze, K. Zhang, Y.-S. Chen, N. Akula, F. Sun, and F. J. McMahon Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome Hum. Mol. Genet., February 1, 2004; 13(3): 335 - 342. [Abstract] [Full Text] [PDF]
|
|