Dynamic programming for single nucleotide polymorphism ID identification in systematic association studies

Kaohsiung Journal of Medical Sciences

Volumn 25, Issue 4, 2009, Pages 165-176

  Yang, Cheng Hong ^a   Chuang, Li Yeh ^b   Cheng, Yu Huei ^a   Wen, Cheng Hao ^c   Chang, Hsueh Wei ^c  

^a NATIONAL KAOHSIUNG UNIVERSITY OF APPLIED SCIENCES   (Taiwan)

^b I SHOU UNIVERSITY   (Taiwan)

^c KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

Author keywords

Association studies; BLAST; BLAT; Dynamic programming; Single nucleotide polymorphisms

Indexed keywords

AMINO ACID; CONTIG; NUCLEOTIDE;

ALGORITHM; ARTICLE; CHROMOSOME; GENE SEQUENCE; INTERNET; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 67650348230     PISSN: 1607551X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1607-551X(09)70057-9     Document Type: Article

References (22)

1. Suh Y, Vijg J. SNP discovery in associating genetic variation with human disease phenotypes. Mutat Res 2005;573:41-53.
2. Erichsen HC, Chanock SJ. SNPs in cancer research and treatment. Br J Cancer 2004;90:747-751
3. Shastry BS. SNPs and haplotypes: genetic markers for disease and drug response (review). Int J Mol Med 2003;11:379-382
4. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics 2002;18:1681-1685 (Pubitemid 36097734)
5. Kang HJ, Choi KO, Kim BD, et al. FESD: a Functional Element SNPs Database in humans. Nucleic Acids Res 2005;33:D518-22. (Pubitemid 40207928)
6. Wang L, Liu S, Niu T, et al. SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management. BMC Bioinformatics 2005;6:60. (Pubitemid 41357955)
7. Staats B, Qi L, Beerman M, et al. Genewindow: an interactive tool for visualization of genomic variation. Nat Genet 2005;37:109-110
8. Savage D, Batley J, Erwin T, et al. SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 2005;33:W493-5. (Pubitemid 44529969)
9. University of Utah Genome Center. GeneSNPs-blast function. Available at: http://www.genome.utah.edu/genesnps/cgi-bin/blast.cgi [Date accessed: August 23, 2006]
10. McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004;32:W20-5. (Pubitemid 38997292)
11. Sherry ST, Ward MH, Kholodov M, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308-311 (Pubitemid 32054478)
12. National Center for Biotechnology Information. SNP-BLAST. Available at: http://www.ncbi.nlm.nih.gov/SNP/snp-hlastByOrg.cgi [Date accessed: January 9, 2009]
13. Eddy SR. What is dynamic programming? Nat Biotechnol 2004;22:909-910
14. Giegerich R. A systematic approach to dynamic programming in bioinformatics. Bioinformatics 2000;16:665-677 (Pubitemid 30843778)
15. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453
16. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402 (Pubitemid 27359211)
17. Yang CH, Chuang LY, Cheng YH, et al. SNP ID-info: SNP ID searching and visualization platform. OMICS 2008;12:217-226
18. Hinrichs AS, Karolchik D, Baertsch R, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006;34:D590-8.
19. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res 2002;12:656-664
20. Zhang K, Qin Z, Chen T, et al. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 2005;21:131-134
21. Su SC, Kuo CC, Chen T. Inference of missing SNPs and information quantity measurements for haplotype blocks. Bioinformatics 2005;21:2001-2007 (Pubitemid 40668038)
22. Chang HW, Yang CH, Chang PL, et al. SNP-RFLPing: restriction enzyme mining for SNPs in genomes. BMC Genomics 2006;7:30.