Reconstructing the Duplication History of a Tandem Repeat

Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology, ISMB 1999

Volumn , Issue , 1999, Pages 44-53

  Benson, Gary ^a   Dong, Lan ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

phylogeny algorithms; tandem repeats

Indexed keywords

ALGORITHMIC SOLUTIONS; DUPLICATION EVENTS; MOST LIKELY; PATTERN OF SUBSTITUTION; PERFORMANCE; PHYLOGENETIC ANALYSIS; PHYLOGENY ALGORITHM; SINGLE SEQUENCES; TANDEM DUPLICATIONS; TANDEM REPEATS;

ARTIFICIAL INTELLIGENCE;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; DNA REPLICATION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; POINT MUTATION; STATISTICAL MODEL; TANDEM REPEAT;

ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; DNA REPLICATION; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; MUTATION; POINT MUTATION; TANDEM REPEAT SEQUENCES;

EID: 0033288057     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. Bell, G., and Torney, D. 1993. Repetitive DNA sequences: some considerations for simple sequence repeats. Computers Chem. 17:185-190.
2. Charles worth, B.; Sniegowski, P.; and Stephan, W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215-220.
3. Di Rienzo, A.; Peterson, A.; Garza, J.; Valdes, A.; Slatkin, M.; and Freimer, N. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 91:3166-3170.
4. Eichler, E.; Hammond, H.; Macpherson, J.; Ward, P.; and Nelson, D. 1995. Population survey of the human FMR1 CGG repeat substructure suggests biased polarity for the loss of AGG interruptions. Human Molecular Genetics 4:2199-2208.
5. Fitch, W. 1971. Toward denning the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.
6. Jeffreys, A.; Tamaki, K.; MacLeod, A.; Monckton, D.; Neil, D.; and Armour, J. 1994. Complex gene conversion events in germline mutation at human minisatellites. Nature Genetics 6:136-145.
7. Kang, S.; Jaworski, A.; Ohshima, K.; and Wells, R. 1995. Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in e. coli. Nature Genetics 10:213-218.
8. Kou, L.; Markowsky, G.; and Berman, L. 1981. A fast algorithm for the Steiner problem in graphs. Acta Inform.. 15:141-145.
9. Kunst, C., and Warren, S. 1994. Cryptic and polar variation of the fragile x repeat could result in predisposing normal alleles. Cell 77:853-861.
10. Levinson, G., and Gutman, G. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molec. Biol. Evol. 4:203-221.
11. Okumura, K.; Kiyama, R.; and Oishi, M. 1987. Sequence analyses of extrachromosomal sau3a and related family DNA: analysis of recombination in the excision event. Nucleic Acids Res. 15:7477-7489.
12. Sankoff, D., and Rousseau, P. 1975. Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming. 9:240-246.
13. Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28:35-42.
14. Schlotterer, C. and Tautz, D. 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 20:211-215.
15. Smith, G. 1976. Evolution of repeated DNA sequences by unequal crossover. Science 191:528-535.
16. Strand, M.; Prolla, T.; Liskay. R.; and Petes, T. 1993. Dcstabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365:274-276.
17. Weitzmann. M.; Woodford, K.: and Usdin, K. 1997. Dna secondary structures and the evolution of hyper-variable tandem arrays. J. of Biological Chemistry 272:9517-9523.
18. Wells, R. 1996. Molecular basis of genetic instability of triplet repeats. J. of Biological Chemistry 271:2875-2878.
19. Zelikovsky. A. 1993. An 11/6-approximation algorithm for the network steincr problem. Algorithmica 9:463-470.