The reversal median problem, common intervals, and mitochondrial gene orders

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

Volumn 4216 LNBI, Issue , 2006, Pages 52-63

  Bernt, Matthias ^a   Merkle, Daniel ^a   Middendorf, Martin ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMBINATORIAL MATHEMATICS; DATA REDUCTION; PROBLEM SOLVING;

BRANCH-AND-BOUND ALGORITHMS; GENE ORDER DATA; REVERSAL MEDIAN PROBLEM (RMP);

GENES;

EID: 33750301368     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11875741_6     Document Type: Conference Paper

References (16)

1. Bérard, S., Bergeron, A., Chauve, C.: Conservation of Combinatorial Structures in Evolution Scenarios. Proc. 2nd RECOMB Workshop. LNBS 3388, (2004) 1-14.
2. Bergeron, A., Blanchette, M., Chateau, A., Chauve, C.: Reconstructing Ancestral Gene Orders Using Conserved Intervals. Proc. WABI. LNCS 3240, (2004) 14-45.
3. Heber, S., Stoye, J.: Algorithms for Finding Gene Clusters. Proc. WABI, LNCS 2149, (2001) 252-263.
4. Sankoff, D.: Edit distance for genome comparison based on non-local operations. Proc. CPU, LNCS 644, (1992) 121-135.
5. Caprara, A.: The Reversal Median Problem. INFORMS Journal on Computing 15(1), (2003) 93-113.
6. Landau, G.M., Parida L., Weimann, O.: Using PQ Trees for Comparative Genomics. Combinatorial Pattern Matching, 16th Annual Symposium, CPM 2005. LNCS 3537, (2005) 128-143.
7. Moret, B.M.E., Tang, J., Warnow, T.: Reconstructing phylogenies from gene-content and gene-order data. Mathematics of Evolution and Phylogeny, Olivier Gascuel editor. Oxford University Press (2004) 321-352.
8. Bourque, G., Pevzner, P.A.: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. (2002) 12(1):26-36,.
9. Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. Genome Informatics (1997) 25-34.
10. Moret, B., Siepel, A.: Finding an Optimal Inversion Median: Experimental Results. Proc. WABI, LNCS 2149, (2001) 189-203.
11. Bernt, M., Merkle, D., Middendorf, M.: Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear.
12. Bergeron, A., Stoye, J.: On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. Proc. COCOON, LNCS, (2003) 68-79.
13. Figeac, M., Varré, J.: Sorting by Reversals with Common Intervals. Proc. WABI. LNBI 3240, (2004) 26-37.
14. Bérard, S., Bergeron, A., Chauve, C., Paul, C.: Perfect sorting by reversals is not always difficult. Proc. WABI, LNCS 3692, (2005) 228-238.
15. Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. In: Proc. 27 Ann. ACM Symp. on Theory of Comput., (1995) 178-189.
16. Boore, J.L.: Mitochondrial database, http://evogen.jgi.doe.gov/ (2005)