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Volumn 20, Issue 4, 2013, Pages 280-295

Ancestral genome organization: An alignment approach

Author keywords

Alignment; Bacillus; Comparative genomics; Duplication; Gene order; Linear programming; Loss; TRNA

Indexed keywords

RIBOSOME RNA;

EID: 84876250832     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0292     Document Type: Article
Times cited : (15)

References (47)
  • 1
    • 84957002571 scopus 로고    scopus 로고
    • Exploring the set of all minimal sequences of reversals-an application to test the replication-directed reversal hypothesis
    • Ajana, Y., Lefebvre, J., Tillier, E., and El-Mabrouk, N. 2002. Exploring the set of all minimal sequences of reversals-an application to test the replication-directed reversal hypothesis. Lect. Notes Comput. Sci. 2452, 300-315.
    • (2002) Lect. Notes Comput. Sci. , vol.2452 , pp. 300-315
    • Ajana, Y.1    Lefebvre, J.2    Tillier, E.3    El-Mabrouk, N.4
  • 2
    • 34250375663 scopus 로고    scopus 로고
    • A general framework for computing rearrangement distances between genomes with duplicates
    • Angibaud, S., Fertin, G., Rusu, I., and Vialette, S. 2007. A general framework for computing rearrangement distances between genomes with duplicates. J. Comput. Biol. 14, 379-393.
    • (2007) J. Comput. Biol. , vol.14 , pp. 379-393
    • Angibaud, S.1    Fertin, G.2    Rusu, I.3    Vialette, S.4
  • 3
    • 33645052751 scopus 로고    scopus 로고
    • The genomic pattern of tDNA operon expression in E. coli
    • Ardell, D., and Kirsebom, L. 2005. The genomic pattern of tDNA operon expression in E. coli. PLoS Comput. Biol. 1, e12.
    • (2005) PLoS Comput. Biol. , vol.1
    • Ardell, D.1    Kirsebom, L.2
  • 4
    • 0034767147 scopus 로고    scopus 로고
    • A fast linear-time algorithm for inversion distance with an experimental comparison
    • Bader, D., Moret, B., and Yan, M. 2001. A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8, 483-491.
    • (2001) J. Comput. Biol. , vol.8 , pp. 483-491
    • Bader, D.1    Moret, B.2    Yan, M.3
  • 5
    • 68649115077 scopus 로고    scopus 로고
    • Formal models of gene clusters
    • In Mandoiu, I. and Zelikovsky, A., eds. Wiley, New York. doi: 10.1002/9780470253441.ch8
    • Bergeron, A., Chauve, C., and Gingras, Y. 2008. Formal models of gene clusters. In Mandoiu, I. and Zelikovsky, A., eds., Bioinformatics Algorithms: Techniques and Applications. Wiley, New York. doi: 10.1002/9780470253441.ch8.
    • (2008) Bioinformatics Algorithms: Techniques and Applications
    • Bergeron, A.1    Chauve, C.2    Gingras, Y.3
  • 6
    • 33846231454 scopus 로고    scopus 로고
    • On the similarity of sets of permutations and its applications to genome comparison
    • Bergeron, A., and Stoye, J. 2003. On the similarity of sets of permutations and its applications to genome comparison. J. Comput. Biol. 13, 1340-1354.
    • (2003) J. Comput. Biol. , vol.13 , pp. 1340-1354
    • Bergeron, A.1    Stoye, J.2
  • 9
    • 36248935185 scopus 로고    scopus 로고
    • Comparing genomes with duplications: A computational complexity point of view. IEEE/ACM Trans
    • Blin, G., Chauve, C., Fertin, G., Rizzi, R., and Vialette, S. 2007. Comparing genomes with duplications: a computational complexity point of view. IEEE/ACM Trans. Comput. Biol. Bioinform. 4, 523-534.
    • (2007) Comput. Biol. Bioinform. , vol.4 , pp. 523-534
    • Blin, G.1    Chauve, C.2    Fertin, G.3    Rizzi, R.4    Vialette, S.5
  • 11
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque, G., and Pevzner, P. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36.
    • (2002) Genome Res. , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.2
  • 12
    • 0032635206 scopus 로고    scopus 로고
    • Formulations and hardness of multiple sorting by reversals
    • Caprara, A. 1999. Formulations and hardness of multiple sorting by reversals. Proc. RECOMB 84-94.
    • (1999) Proc. RECOMB , pp. 84-94
    • Caprara, A.1
  • 14
    • 57149085266 scopus 로고    scopus 로고
    • A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes
    • Chauve, C., and Tannier, E. 2008. A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4, e1000234.
    • (2008) PLoS Comput. Biol. , vol.4
    • Chauve, C.1    Tannier, E.2
  • 15
    • 33746238850 scopus 로고    scopus 로고
    • The approximability of the exemplar breakpoint distance problem
    • Chen, Z., Fu, B., and Zhu, B. 2006. The approximability of the exemplar breakpoint distance problem. Lect. Notes Comput. Sci. 4041, 291-302.
    • (2006) Lect. Notes Comput. Sci. , vol.4041 , pp. 291-302
    • Chen, Z.1    Fu, B.2    Zhu, B.3
  • 16
    • 19644386079 scopus 로고    scopus 로고
    • Rates and patterns of gene duplication and loss in the human genome
    • Cotton, J., and Page, R. 2005. Rates and patterns of gene duplication and loss in the human genome. Proc. R. Soci. Lond. Ser. B 272, 277-283.
    • (2005) Proc. R. Soci. Lond. Ser. B , vol.272 , pp. 277-283
    • Cotton, J.1    Page, R.2
  • 19
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong, H., Nilsson, L., and Kurland, C.G. 2006. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260, 649-663.
    • (2006) J. Mol. Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 20
    • 0042027896 scopus 로고    scopus 로고
    • Structural dynamics of eukaryotic chromosome evolution
    • Eichler, E., and Sankoff, D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301, 793-797.
    • (2003) Science , vol.301 , pp. 793-797
    • Eichler, E.1    Sankoff, D.2
  • 21
    • 0034568798 scopus 로고    scopus 로고
    • Evidence for symmetric chromosomal inversions around the relication origin in bacteria
    • research
    • Eisen, J., Heidelberg, J., White, O., and Salzberg, S. 2000. Evidence for symmetric chromosomal inversions around the relication origin in bacteria. Genome Biol. 1, research0011.1-0011.9.
    • (2000) Genome Biol , vol.1 , pp. 1-9
    • Eisen, J.1    Heidelberg, J.2    White, O.3    Salzberg, S.4
  • 22
    • 19544375644 scopus 로고    scopus 로고
    • Genome rearrangement with gene families
    • In: Oxford University Press, Oxford, UK
    • El-Mabrouk, N. 2005. Genome rearrangement with gene families 291-320. In: Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford, UK.
    • (2005) Mathematics of Evolution and Phylogeny , pp. 291-320
    • El-Mabrouk, N.1
  • 24
    • 36048950933 scopus 로고    scopus 로고
    • Gene family evolution across 12 Drosophila genomes
    • Hahn, M., Han, M., and Han, S.-G. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3, e197.
    • (2007) PLoS Genet. , vol.3
    • Hahn, M.1    Han, M.2    Han, S.-G.3
  • 26
    • 0002856077 scopus 로고    scopus 로고
    • Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
    • Hannenhalli, S., and Pevzner, P.A. 1999. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). J. ACM 48, 1-27.
    • (1999) J. ACM , vol.48 , pp. 1-27
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 27
    • 78649939271 scopus 로고    scopus 로고
    • The zero exemplar distance problem
    • Jiang, M. 2010. The zero exemplar distance problem. Proc. RECOMB-CG 74-82.
    • (2010) Proc. RECOMB-CG , pp. 74-82
    • Jiang, M.1
  • 28
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacoillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
    • Kanaya, S., Yamada, Y., Kudo, Y., and Ikemura, T. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacoillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238, 143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 29
    • 80053031739 scopus 로고    scopus 로고
    • A practical algorithm for ancestral rearrangement reconstruction
    • Kovac, J., Brejova, B., and Vinar, T. 2011. A practical algorithm for ancestral rearrangement reconstruction. Lect. Notes Bioinform. 6833, 163-174.
    • (2011) Lect. Notes Bioinform. , vol.6833 , pp. 163-174
    • Kovac, J.1    Brejova, B.2    Vinar, T.3
  • 30
    • 33645000532 scopus 로고    scopus 로고
    • Gene proximity analysis across whole genomes via PQ trees
    • Landau, G., Parida, L., and Weimann, O. 2005. Gene proximity analysis across whole genomes via PQ trees. J. Comput. Biol. 12, 1289-1306.
    • (2005) J. Comput. Biol. , vol.12 , pp. 1289-1306
    • Landau, G.1    Parida, L.2    Weimann, O.3
  • 31
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M., and Conery, J. 2000. The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.2
  • 33
    • 0035229986 scopus 로고    scopus 로고
    • New approaches for reconstructing phylogenies from gene order data
    • Moret, B., Wang, L., Warnow, T., and Wyman, S. 2001. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17, S165-S173.
    • (2001) Bioinformatics , vol.17
    • Moret, B.1    Wang, L.2    Warnow, T.3    Wyman, S.4
  • 35
    • 4544280334 scopus 로고    scopus 로고
    • The median problems for breakpoints are NP-complete
    • Complexity
    • Pe'er, I., and Shamir, R. 1998. The median problems for breakpoints are NP-complete. Proc. Elec. Colloq. Comput. Complexity 71.
    • (1998) Proc. Elec. Colloq. Comput , pp. 71
    • Pe'Er, I.1    Shamir, R.2
  • 36
    • 0347364639 scopus 로고    scopus 로고
    • Changing identities: Trna duplication and remolding within animal mitochondrial genomes
    • Rawlings, T., Collins, T., and Bieler, R. 2003. Changing identities: trna duplication and remolding within animal mitochondrial genomes. Proc. Natl. Acad. Sci. USA 100: 15700-15705.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15700-15705
    • Rawlings, T.1    Collins, T.2    Bieler, R.3
  • 38
    • 34247376550 scopus 로고    scopus 로고
    • Anticodon-dependent conservation of bacterial tRNA gene sequences
    • Saks, M., and Conery, J. 2007. Anticodon-dependent conservation of bacterial tRNA gene sequences. RNA 13, 651-660.
    • (2007) RNA , vol.13 , pp. 651-660
    • Saks, M.1    Conery, J.2
  • 39
    • 0033391532 scopus 로고    scopus 로고
    • Genome rearrangements with gene families
    • Sankoff, D. 1999. Genome rearrangements with gene families. Bioinformatics 15, 909-917.
    • (1999) Bioinformatics , vol.15 , pp. 909-917
    • Sankoff, D.1
  • 40
    • 84947708594 scopus 로고    scopus 로고
    • The median problem for breakpoints in comparative genomics
    • Sankoff, D., and Blanchette, M. 1997. The median problem for breakpoints in comparative genomics. Lect. Notes Comput. Sci. 1276, 251-263.
    • (1997) Lect. Notes Comput. Sci. , vol.1276 , pp. 251-263
    • Sankoff, D.1    Blanchette, M.2
  • 41
    • 76749129703 scopus 로고    scopus 로고
    • MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
    • Shi, G., Zhang, L., and Jiang, T. 2010. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics 11, 10.
    • (2010) BMC Bioinformatics , vol.11 , pp. 10
    • Shi, G.1    Zhang, L.2    Jiang, T.3
  • 43
    • 65649136238 scopus 로고    scopus 로고
    • Analysis of the complement and molecular evolution of tRNA genes in cow
    • Tang, D., Glazov, E., McWilliam, S., Barris, W., and Dalrymple, B. 2009. Analysis of the complement and molecular evolution of tRNA genes in cow. BMC Genomics 10, 188.
    • (2009) BMC Genomics , vol.10 , pp. 188
    • Tang, D.1    Glazov, E.2    McWilliam, S.3    Barris, W.4    Dalrymple, B.5
  • 44
    • 65849156401 scopus 로고    scopus 로고
    • Multichromosomal median and halving problems under different genomic distances
    • Tannier, E., Zheng, C., and Sankoff, D. 2009. Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120.
    • (2009) BMC Bioinformatics , vol.10 , pp. 120
    • Tannier, E.1    Zheng, C.2    Sankoff, D.3
  • 45
    • 0033776631 scopus 로고    scopus 로고
    • Genome rearrangement by replication-directed translocation
    • Tillier, E., and Collins, R. 2000. Genome rearrangement by replication-directed translocation. Nat. Genet. 26, 134-135.
    • (2000) Nat. Genet. , vol.26 , pp. 134-135
    • Tillier, E.1    Collins, R.2
  • 46
    • 34548501747 scopus 로고    scopus 로고
    • Natural history and evolutionary principles of gene duplication in fungi
    • Wapinski, I., Pfeffer, A., Friedman, N., and Regev, A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54-61.
    • (2007) Nature , vol.449 , pp. 54-61
    • Wapinski, I.1    Pfeffer, A.2    Friedman, N.3    Regev, A.4
  • 47
    • 33646886152 scopus 로고    scopus 로고
    • Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
    • Withers, M., Wernisch, L., and Reis, M.D., 2006. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. Bioinformatics 12, 933-942.
    • (2006) Bioinformatics , vol.12 , pp. 933-942
    • Withers, M.1    Wernisch, L.2    Reis, M.D.3


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