Genome rearrangements and sorting by reversals

SIAM Journal on Computing

Volumn 25, Issue 2, 1996, Pages 272-289

  Bafna, Vineet ^a   Pevzner, Pavel A ^a  

^a Pennsylvania State University   (United States)

Author keywords

Computational molecular biology; Genome rearrangements; Sorting by reversals

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; BIOLOGY; CHROMOSOMES; COMPUTER SCIENCE; CONFORMAL MAPPING; DNA; GENES;

COMPUTATIONAL MOLECULAR BIOLOGY; GENOME ARRANGEMENTS; GOLLAN CONJECTURE; MOLECULAR EVOLUTION; RANDOM PERMUTATIONS; SORTING BY REVERSALS;

COMPUTATIONAL METHODS;

EID: 0030130366     PISSN: 00975397     EISSN: None     Source Type: Journal    
DOI: 10.1137/S0097539793250627     Document Type: Article

References (31)

1. M. AIGNER AND D. B. WEST, Sorting by insertion of leading element, J. Combin. Theory Ser. A, 45 (1987), pp. 306-309.
2. N. AMATO, M. BLUM, S. IRANI, AND R. RUBINFELD, Reversing trains: A turn of the century sorting problem, J. Algorithms, 10 (1989), pp. 413-428.
3. V. BAFNA AND P. PEVZNER, Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome, Molec. Biol. Evolution, 12 (1995), pp. 239-246.
4. T. H. CORMEN, C. E. LEISERSON, AND R. L. RIVEST, Introduction to Algorithms, MIT Press, Cambridge, MA, 1990.
5. S. EVEN AND O. GOLDREICH, The minimum-length generator sequence problem is NP-hard, J. Algorithms, 2 (1981), pp. 311-313.
6. C. FAURON AND M. HAVLIK, The maize mitochondrial genome of the normal type and the cytoplasmic male sterile type T have very different organization, Current Genetics, 15 (1989), pp. 149-154.
7. W. H. GATES AND C. H. PAPADIMITRIOU, Bounds for sorting by prefix reversals, Discrete Math., 27 (1979), pp. 47-57.
8. E. GYORI AND E. TURAN, Stack of pancakes, Studia Sci. Math. Hungar., 13 (1978), pp. 133-137.
9. S. HANNENHALLI, C. CHAPPEY, E. KOONIN, AND P. PEVZNER, Genome sequence comparison and scenarios for genome rearrangement: A test case, Genomics, (1995).
10. R. J. HOFFMANN, J. L. BOORE, AND W. M. BROWN, A novel mitochondrial genome organization for the blue mussel, Mytilus edulis, Genetics, 131 (1992), pp. 397-412.
11. 5/2 algorithm for maximum matching in bipartite graphs, SIAM J. Comput., 2 (1973), pp. 225-231.
12. S. B. HOOT AND J. D. PALMER, Structural rearrangements including parallel inversions within the chloroplast genome of anemone and related genera, J. Molec. Evolution, 38 (1994), pp. 274-281.
13. M. R. JERRUM, The complexity of finding minimum-length generator sequences, Theoret. Comput. Sci., 36 (1985), pp. 265-289.
14. S. KARLIN, E. S. MOCARSKI, AND G. A. SCHACHTEL, Molecular evolution of herpesviruses: Genomic and protein sequence comparisons, J. Virology, 68 (1994), pp. 1886-1902.
15. J. KECECIOGLU AND D. SANKOFF, Exact and approximation algorithms for the reversal distance between two permutations, Proc. 4th Annual Symposium on Combinatorial Pattern Matching, A. Apostolico, M. Crochemore, Z. Galil, and U. Manber, eds., Padova, Italy, 1993; Lecture Notes in Comput. Sci., 684 (1993), pp. 87-105; Algorithmica, 13 (1995), pp. 180-210.
16. J. KECECIOGLU AND D. SANKOFF, Exact and approximation algorithms for the reversal distance between two permutations, Proc. 4th Annual Symposium on Combinatorial Pattern Matching, A. Apostolico, M. Crochemore, Z. Galil, and U. Manber, eds., Padova, Italy, 1993; Lecture Notes in Comput. Sci., 684 (1993), pp. 87-105; Algorithmica, 13 (1995), pp. 180-210.
17. J. KECECIOGLU AND D. SANKOFF, Exact and approximation algorithms for the reversal distance between two permutations, Proc. 4th Annual Symposium on Combinatorial Pattern Matching, A. Apostolico, M. Crochemore, Z. Galil, and U. Manber, eds., Padova, Italy, 1993; Lecture Notes in Comput. Sci., 684 (1993), pp. 87-105; Algorithmica, 13 (1995), pp. 180-210.
18. _, Efficient bounds for oriented chromosome inversion distance, Proc. 5th Annual Symposium on Combinatorial Pattern Matching, M. Crochemore and D. Gusfield, eds., Asilomar, CA, 1994; Lecture Notes in Comput. Sci., 807 (1994), pp. 307-325.
19. _, Efficient bounds for oriented chromosome inversion distance, Proc. 5th Annual Symposium on Combinatorial Pattern Matching, M. Crochemore and D. Gusfield, eds., Asilomar, CA, 1994; Lecture Notes in Comput. Sci., 807 (1994), pp. 307-325.
20. E.B. KNOX, S. R. DOWNIE, AND J. D. PALMER, Chloroplast genome rearrangements and evolution of giant lobelias from herbaceous ancestors, Molec. Biol. Evolution, 10 (1993), pp. 414-430.
21. E. V. KOONIN AND V. V. DOLJA, Evolution and taxonomy of positive-strand RNA viruses: Implications of comparative analysis of amino acid sequences, Crit. Rev. Biochem. Molec. Biol., 28 (1993), pp. 375-430.
22. A. KOTZIG, Moves without forbidden transitions in a graph, Mat. Casopis, 18 (1968), pp. 76-80.
23. M. F. LYON, X-chromosome inactivation and the location and expression of X-linked genes, Amer. J. Human Genetics, 42 (1988), pp. 8-16.
24. J. D. PALMER AND L. HERBON, Unicircular structure of the Brassica hirta mitochondrial genome, Current Genetics, 11 (1987), pp. 565-570.
25. _, Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence, J. Molec. Evolution, 27 (1988), pp. 65-74.
26. P. PEVZNER, DNA physical mapping and alternating Eulerian cycles in colored graphs, Algorithmica, 13 (1995), pp. 77-105.
27. L. A. RAUBESON AND R. K. JANSEN, Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants, Science, 255 (1992), pp. 1697-1699.
28. D. SANKOFF, G. LEDUC, N. ANTOINE, B. PAQUIN, B. F. LANG, AND R. CEDERGREN, Gene order comparisons for phylogenetic inference: Evolution of the mitchondrial genome, Proc. Natl. Acad. Sci. U.S.A, 89 (1992), pp. 6575-6579.
29. D. SANKOFF, Analytical approaches to genomic evolution, Biochimie, 75 (1993), pp. 409-413.
30. J. WHITING, M. PLILEY, J. FARMER, AND D. JEFFERY, In situ hybridization analysis of chromosomal homologies in Drosophila melanogaster and Drosophila virilis, Genetics, 122 (1989), pp. 99-109.
31. G. A. WATTERSON, W. J. EWENS, T. E. HALL, AND A. MORGAN, The chromosome inversion problem, J. Theoret. Biol., 99 (1982), pp. 1-7.