Conserved interval distance computation between non-trivial genomes

Lecture Notes in Computer Science

Volumn 3595, Issue , 2005, Pages 22-31

  Blin, Guillaume ^a   Rizzi, Romeo ^b  

^a UNIVERSITÉ DE NANTES   (France)

^b UNIVERSITY OF TRENTO   (Italy)

Author keywords

Computational complexity; Conserved interval distance; Duplicated genes; Exemplar string; Longest Common Substring; Matching

Indexed keywords

BIOTECHNOLOGY; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; COMBINATORIAL MATHEMATICS;

CONSERVED INTERNAL DISTANCE; DUPLICATED GENES; EXEMPLER STRING; LONGEST COMMON SUBSTRING; MATCHING; CONSERVED INTERVALS; EXEMPLAR STRING;

GENES;

EID: 26844563692     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11533719_5     Document Type: Conference Paper

References (12)

1. A. Bergeron and J. Stoye. On the similarity of sets of permutations and its applications to genome comparison. Proceedings of COCOON 03, 2697 of LNCS:68-79, 2003.
2. M. Blanchette, T. Kunisawa, and D. Sankoff. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49(2): 193-203, 1999.
3. G. Blin, C. Chauve, and G. Fertin. The breakpoints distance for signed sequences. In Actes de CompBioNets 2004, volume 3 of Texts in Algorithms, pages 3-16. KCL Publications, 2004.
4. G. Bourque and P. A. Pevzner. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res., 12(1):26-36, 2002.
5. G. Bourque, P.A. Pevzner, and G. Tesler. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse and rat genomes. Genome Res., 14(4):507-516, 2004.
6. D. Bryant. The complexity of calculating exemplar distances. In D. Sankoff and J. Nadeau, editors, Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pages 207-212. Kluwer Acad. Pub., 2000.
7. M. Garey and D. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman and Company, 1979.
8. O. Gascuel, editor. Mathematics of Evolution and Phylogeny. Oxford Univ. Press, 2004. To appear.
9. M. Marron, K.M. Swenson, and B.M.E. Moret. Genomic distances under deletions and inversions. Proceedings of COCOON 03, 2697 of LNCS:537-547, 2003.
10. B. M. E. Moret, A. C. Siepel, J. Tang, and T. Liu. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In WABI 2002, volume 2452 volume of LNCS, pages 521-536. Springer Verlag, 2002.
11. D. Sankoff. Genome rearrangement with gene families. Bioinformatics, 15(11):909-917, 1999.
12. K.M. Swenson, M. Marron, J.E Earnest-DeYoung, and B.M.E. Moret. Approximating the true evolutionary distance between two genomes. Technical Report TR-CS2004-15, Department of Computer Science, University of New Mexico, 2004.