Exemplar longest common subsequence

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 4, Issue 4, 2007, Pages 535-543

  Bonizzoni, Paola ^a   Della Vedova, Gianluca ^a   Dondi, Riccardo ^b   Fertin, Guillaume ^c   Rizzi, Raffaella ^a   Vialette, Stéphane ^d  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF BERGAMO   (Italy)

^c UNIVERSITÉ DE NANTES   (France)

^d UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

Algorithm design and analysis; Analysis of algorithms; Combinatorial algorithms; Comparative genomics; Longest common subsequence; Problem complexity

Indexed keywords

APPROXIMATION THEORY; DNA SEQUENCES; PROBLEM SOLVING;

ALGORITHM DESIGN AND ANALYSIS; ANALYSIS OF ALGORITHMS; COMBINATORIAL ALGORITHMS; COMPARATIVE GENOMICS; LONGEST COMMON SUBSEQUENCE; PROBLEM COMPLEXITY;

COMPUTATIONAL COMPLEXITY;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER; COMPUTER PROGRAM; DNA SEQUENCE; METHODOLOGY; STATISTICAL ANALYSIS; STATISTICAL MODEL; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTERS; DATA INTERPRETATION, STATISTICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 36248966478     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.1066     Document Type: Conference Paper

References (16)

1. P. Alimonti and V. Kann, "Some APX-Completeness Results for Cubic Graphs," Theoretical Computer Science, vol. 237, nos. 1-2, pp. 123-134, 2000.
2. B. Aspvall, M.F. Plass, and R.E. Tarjan, "A Linear-Time Algorithm for Testing the Truth of Certain Quantified Boolean Formulas," Information Processing Letters, vol. 8, no. 3, pp. 121-123, 1979.
3. T.H. Cormen, C.E. Leiserson, R.L. Rivest, and C. Stein, Introduction to Algorithms, second ed. MIT Press, 2001.
4. K. Hakata and H. Imai, "The Longest Common Subsequence Problem for Small Alphabet Size between Many Strings," Proc. Third Int'l Symp. Algorithms and Computation (ISAAC '92), pp. 469-478, 1992.
5. W. Hsu and M. Du, "New Algorithms for the LCS Problem," J. Computer and System Sciences, vol. 19, pp. 133-152, 1984.
6. T. Jiang and M. Li, "On the Approximation of Shortest Common Supersequences and Longest Common Subsequences," SIAM J. Computing, vol. 24, no. 5, pp. 1122-1139, 1995.
7. D. Maier, "The Complexity of Some Problems on Subsequences and Supersequences," J. ACM, vol. 25, pp. 322-336, 1978.
8. A. Bergeron and J. Stoye, "On the Similarity of Sets of Permutations and Its Applications to Genome Comparison," Proc. Ninth Int'l Computing and Combinatorics Conf. (COCOON '03), pp. 68-79, 2003.
9. T. Uno and M. Yagiura, "Fast Algorithms to Enumerate All Common Intervals of Two Permutations," Algorithmica, vol. 2, pp. 290-309, 2000.
10. D. Sankoff and L. Haque, "Power Boosts for Cluster Tests," Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB) Int'l Workshop Comparative Genomics (RCG '05), pp. 121-130, 2005.
11. D. Sankoff, "Genome Rearrangement with Gene Families," Bioinformatics, vol. 11, pp. 909-917, 1999.
12. G. Blin, C. Chauve, and G. Fertin, "The Breakpoint Distance for Signed Sequences," Proc. First Int'l Conf. Algorithms and Computational Methods for Biochemical and Evolutionary Networks (CompBio Nets '04), pp. 3-16, 2004.
13. D. Bryant, "The Complexity of Calculating Exemplar Distances," Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., pp. 207-212, 2000.
14. G. Blin and R. Rizzi, "Conserved Interval Distance Computation between Non-Trivial Genomes," Proc. 11th Int'l Computing and Combinatorics Conf. (COCOON '05), pp. 22-31, 2005.
15. C. Chauve, G. Fertin, R. Rizzi, and S. Vialette, "Genomes Containing Duplicates Are Hard to Compare," Proc. Int'l Workshop Bioinformatics Research and Applications (IWBRA '06), pp. 783-790, 2006.
16. R.A. Wagner and M.J. Fischer, "The String-to-String Correction Problem," J. ACM, vol. 21, no. 1, pp. 168-173, 1974.