Rearrangement phylogeny of genomes in contig form

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

Volumn 5542, Issue , 2009, Pages 160-172

  Mũnoz, Adriana ^a   Sankoff, David ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMAL LOCATION; CONTIGS; GENE ORDERS; GENOME SEQUENCING; GENOMIC DISTANCE; PHYLOGENETIC ANALYSIS;

BIOLOGY;

BIOINFORMATICS;

EID: 67650166631     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-01551-9_17     Document Type: Conference Paper

References (14)

1. Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163-173. Springer, Heidelberg (2006) (Pubitemid 44609667)
2. Bhutkar, A., Gelbart, W.M., Smith, T.: Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. Genome Biology 8, R236 (2007)
3. Bhutkar, A., Schaeffer, S.W., Russo, S.M., Xu, M., Smith, T.F., Gelbart, W.: Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics 179, 1657-1680 (2008)
4. Dalevi, D., Eriksen, N.: Expected gene-order distances and model selection in bacteria. Bioinformatics 24, 1332-1338 (2008) (Pubitemid 351737137)
5. Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007)
6. Eriksen, N., Hultman, A.: Estimating the expected reversal distance after a fixed number of reversals. Advances in Applied Mathematics 32, 439-453 (2004) (Pubitemid 38457666)
7. Gaul, E., Blanchette, M.: Ordering partially assembled genomes using gene arrangements. In: Bourque, G., El-Mabrouk, N. (eds.) RECOMB-CG 2006. LNCS (LNBI), vol. 4205, pp. 113-128. Springer, Heidelberg (2006) (Pubitemid 44641564)
8. Krzywinski, J., Grushko, O.G., Besansky, N.: Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Molecular Phylogenetics and Evolution 39, 417-423 (2006)
9. Sankoff, D., Zheng, Wall, C.P.K., de Pamphilis, C.W., Leebens-Mack, J., Albert, V.A.: Internal validation of ancestral gene order reconstruction in angiosperm phylogeny. In: Vialette, S., Nelson, C. (eds.) RECOMB-CG 2008. LNCS, vol. 5267, pp. 252-264. Springer, Heidelberg (2008)
10. Savard, J., Tautz, D., Richards, S., Weinstock, G.M., Gibbs, R.A., Werren, J.H., Tettelin, H., Lercher, M.J.: Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Research 16, 1334-1338 (2006) (Pubitemid 44664675)
11. Severson, D.W., DeBruyn, B., Lovin, D.D., Brown, S.E., Knudson, D.L., Morlais, I.: Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae. Journal of Heredity 95, 103-113 (2004) (Pubitemid 38509726)
12. Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences 65, 587-609 (2002)
13. Wang, L.-S., Warnow, T.: Distance-based genome rearrangement phylogeny. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny, ch. 13, Oxford, pp. 353-383 (2005)
14. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346 (2005) (Pubitemid 41222437)