Algorithms for finding gene clusters

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2149, Issue , 2001, Pages 252-263

  Heber, Steffen ^a   Stoye, Jens ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; GENES;

CIRCULAR PERMUTATION; COMMON INTERVALS; GENE CLUSTERS; GENE ORDERS; K PERMUTATIONS; LINEAR SPACES; SIGNED PERMUTATIONS; TIME COMPLEXITY;

CLUSTERING ALGORITHMS;

EID: 84959048279     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-44696-6_20     Document Type: Conference Paper

References (26)

1. V. Bafna and P. Pevzner. Genome rearrangements and sorting by reversals. SIAM J. Computing, 25(2):272–289, 1996.
2. K. S. Booth and G. S. Lueker. Testing for the consecutive ones property, interval graphs and graph planarity using PQ-tree algorithms. J. Comput. Syst. Sci., 13(3):335–379, 1976.
3. R. M. Brady. Optimization strategies gleaned from biological evolution. Nature, 317:804–806, 1985.
4. T. Dandekar, B. Snel, M. Huynen, and P. Bork. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23(9):324–328, 1998.
5. J. A. Eisen. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev., 10(6):606–611, 2000.
6. W. Fujibuchi, H. Ogata, H. Matsuda, and M. Kanehisa. Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res., 28(20):4029–4036, 2000.
7. D. Fulkerson and O. Gross. Incidence matrices with the consecutive 1s property. Bull. Am. Math. Soc., 70:681–684, 1964.
8. M. C. Golumbic. Algorithmic Graph Theory and Perfect Graphs. Academic Press, New York, 1980.
9. S. Hannenhalli and P. A. Pevzner. Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. J. ACM, 46(1):1–27, 1999.
10. S. Heber and J. Stoye. Finding all common intervals of k permutations. In Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching, CPM 2001, volume 2089 of Lecture Notes in Computer Science, pages 207–219. Springer Verlag, 2001. To appear.
11. M. A. Huynen and P. Bork. Measuring genome evolution. Proc. Natl. Acad. Sci. USA, 95(11):5849–5856, 1998.
12. M. A. Huynen, B. Snel, and P. Bork. Inversions and the dynamics of eukaryotic gene order. Trends Genet., 17(6):304–306, 2001.
13. H. Kaplan, R. Shamir, and R. E. Tarjan. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Computing, 29(3):880–892, 1999.
14. J. D. Kececioglu and D. Sankoff. Efficient bounds for oriented chromosome inversion distance. In M. Crochemore and D. Gusfield, editors, Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching, CPM 94, volume 807 of Lecture Notes in Computer Science, pages 307–325. Springer Verlag, 1994.
15. S. Kobayashi, I. Ono, and M. Yamamura. An efficient genetic algorithm for job shop scheduling problems. In Proc. of the 6th International Conference on Genetic Algorithms, pages 506–511. Morgan Kaufmann, 1995.
16. W. C. III Lathe, B. Snel, and P. Bork. Gene context conservation of a higher order than operons. Trends Biochem. Sci., 25(10):474–479, 2000.
17. E. M. Marcotte, M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. Detecting protein function and protein-protein interactions from genome sequences. Science, 285:751–753, 1999.
18. H. Mühlenbein, M. Gorges-Schleuter, and O. Kramer. Evolution algorithms in combinatorial optimization. Parallel Comput., 7:65–85, 1988.
19. A. R. Mushegian and E. V. Koonin. Gene order is not conserved in bacterial evolution. Trends Genet., 12(8):289–290, 1996.
20. R. Overbeek, M. Fonstein, M. D’Souza, G. D. Pusch, and N. Maltsev. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA, 96(6):2896–2901, 1999.
21. P. A. Pevzner. Computational Molecular Biology: An Algorithmic Approach. MIT Press, Cambridge, MA, 2000.
22. B. Snel, G. Lehmann, P. Bork, and M. A. Huynen. STRING: A web-server to retrieve and display the repeatedly occurring neigbourhood of a gene. Nucleic Acids Res., 28(18):3443–3444, 2000.
23. J. Tamames, G. Casari, C. Ouzounis, and A. Valencia. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol., 44(1):66–73, 1997.
24. J. Tamames, M. Gonzalez-Moreno, J. Mingorance, A. Valencia, and M. Vicente. Bringing gene order into bacterial shape. Trends Genet., 17(3):124–126, 2001.
25. R. L. Tatusov, A. R. Mushegian, P. Bork, N.P. Brown, W. S. Hayes, M. Borodovsky, K. E. Rudd, and E. V. Koonin. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol., 6:279–291, 1996.
26. T. Uno and M. Yagiura. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica, 26(2):290–309, 2000.