Tandem cyclic alignment

Discrete Applied Mathematics

Volumn 146, Issue 2, 2005, Pages 124-133

  Benson, Gary ^a  

^a BOSTON UNIVERSITY   (United States)

Author keywords

Cyclic alignment; Tandem repeats; Wraparound dynamic programming

Indexed keywords

ALGORITHMS; CODES (SYMBOLS); COSTS; DATABASE SYSTEMS; DYNAMIC PROGRAMMING; FUNCTIONS; GENES;

CYCLIC ALIGNMENT; FINGERPRINTING; TANDEM REPEATS; WRAPAROUND DYNAMIC PROGRAMMING;

PROBLEM SOLVING;

EID: 11844273816     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2004.04.009     Document Type: Conference Paper

References (22)

1. K. Alakurtti, K. Virtaneva, T. Joensuu, J. Palvimo, and A. Lehesjoki Characterization of the cystatin B gene promoter harboring the dodecamer repeat expanded in progressive myoclonus epilepsy EPM1, Gene 242 2000 65 73
2. S.T. Bennett, A.M. Lucassen, S.C.L. Gough, E.E. Powell, D.E. Undlien, L.E. Pritchard, M.E. Merriman, Y. Kawaguchi, M.J. Dronsfield, F. Pociot, J. Nerup, N. Bouzekri, A. Thomsen, K.S. Ronningen, A.H. Barnett, S.C. Bain, and J.A. Todd Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus Nature Genetics 9 1995 284 292
3. G. Benson Tandem repeats finder a program to analyze DNA sequences Nucleic Acids Res. 27 1999 573 580
4. V. Fischetti, G. Landau, J. Schmidt, P. Sellers, Identifying periodic occurrences of a template with applications to a protein structure, in: A. Apostolico, M. Crochemore, Z. Galil, U. Manber (Eds.), Proceedings of the 3rd Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, vol. 644, Springer, Berlin, 1992, pp. 111-120.
5. P. Le Flche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse, and G. Vergnaud A tandem repeats database for bacterial genomes application to the genotyping of Yersinia pestis and Bacillus anthracis BMC Microbiol. 1 2001 2
6. Y.-H. Fu, A. Pizzuti, R.G. Fenwick Jr., J. King, S. Rajnarayan, P.W. Dunne, J. Dubel, G.A. Nasser, T. Ashizawa, P. DeJong, B. Wieringa, R. Korneluk, M.B. Perryman, H.F. Epstein, and C.T. Caskey An unstable triplet repeat in a gene related to myotonic muscular dystrophy Science 255 1992 1256 1258
7. S. Gosse-Brun, S. Sauvaigo, A. Daver, M. Page, A. Lortholary, F. Larra, Y. Bignon, and D. Bernard-Gallon Specific H-Ras minisatellite alleles in breast cancer susceptibility Anticancer Res. 19 1999 5191 5196
8. Huntington's disease collaborative research group, A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes, Cell 72 (1993) 971-983.
9. P. Keim, L. Price, A. Klevytska, K. Smith, J. Schupp, R. Okinaka, P. Jackson, and M. Hugh-Jones Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis J. Bacteriol. 182 2000 2928 2936
10. M.D. Lalioti, H.S. Scott, C. Buresit, C. Rossier, A. Bottani, M.A. Morris, A. Malafosse, and S.E. Antonarakis Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy Nature 386 1997 847 851
11. G.M. Landau, E.W. Myers, and J.P. Schmidt Incremental string comparison SIAM J. Comput. 27 1998 7 82
12. V.I. Levenshtein Binary codes capable of correcting deletions, insertions and reversals Soviet Phys. Dokl. 10 1966 707 710
13. M. Maes On a cyclic string-to-string correction problem Inform. Process. Lett. 35 1990 73 78
14. W. Miller, and E. Myers Approximate matching of regular expressions Bull. Math. Biol. 51 1989 5 37
15. E. Myers An O(ND) difference algorithm and its variants Algorithmica 1 1986 251 266
16. D. Owerbach, and K.H. Gabbay Localization of a type 1 diabetes susceptibility locus to the variable tandem repeat region flanking the insulin gene Diabetes 42 1993 1708 1714
17. C.M. Phelan, T.R. Rebbeck, B.L. Weber, P. Deville, M.H. Ruttledge, H.T. Lynch, G.M. Lenoir, M.R. Stratton, D.F. Easton, B.A.J. Ponder, L. Albright, C. Larsson, D.E. Goldgar, and S.A. Narod Ovarian cancer risk in BRCA1 carriers is modified by the HRAS1 variable number of tandem repeat (VNTR) locus Nature Genetics 12 1996 309 311
18. J. Schmidt All shortest paths in weighted grid graphs and its application to finding all approximate repeats in strings SIAM J. Comput. 27 1998 972 992
19. A. Verkerk, M. Pieretti, J. Sutcliffe, Y. Fu, D. Kuhl, A. Pizzuti, O. Reiner, S. Richards, M. Victoria, F. Zhang, B. Eussen, G. van Ommen, A. Blonden, G. Riggins, J. Chastain, C. Kunst, H. Galjaard, C. Caskey, D. Nelson, B. Oostra, and S. Warren Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome Cell 65 1991 905 914
20. K. Virtaneva, E. D'Amato, J. Miao, M. Koskiniemi, R. Norio, G. Avanzini, S. Franceschetti, R. Michelucci, C.A. Tassinari, S. Omer, L.A. Pennacchio, R.M. Myers, J.L. Dieguez-Lucena, R. Krahe, A. de la Chapelle, and A. Lehesjoki Unstable minisatellite expansion causing recessively inherited myoclonus epilepsy, EPM1 Nature Genetics 15 1997 393 396
21. R.A. Wagner, and M.J. Fischer The string-to-string correction problem J. Assoc. Comput. Mach. 21 1974 168 173
22. J. Weitzel, S. Ding, G. Larson, R. Nelson, A. Goodman, E. Grendys, H. Ball, and T. Krontiris HRAS1 minisatellite locus and risk of ovarian cancer Cancer Res. 60 2000 259 261