메뉴 건너뛰기




Volumn 15, Issue 8, 2008, Pages 1079-1092

Improving reversal median computation using commuting reversals and cycle information

Author keywords

Algorithms; Combinatorial optimization; Computational molecular biology; Genomic rearrangements; Phylogenetic analyses

Indexed keywords

CHROMOSOME ANALYSIS; CONFERENCE PAPER; GENE REARRANGEMENT; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC DISTANCE; MATHEMATICAL GENETICS; PHYLOGENY; PRIORITY JOURNAL;

EID: 52449096724     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0116     Document Type: Conference Paper
Times cited : (3)

References (27)
  • 1
    • 0034767147 scopus 로고    scopus 로고
    • A fast linear-time algorithm for reversal distance with an experimental comparison
    • Bader, D., Moret, B., and Yan, M. 2001. A fast linear-time algorithm for reversal 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
  • 2
    • 19544374490 scopus 로고    scopus 로고
    • Genome rearrangement distances and gene order phylogeny in γ-proteobacteria
    • Belda, E., Moya, A., and Silva, F. 2005. Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol. Biol. Evol. 22, 1456-1467.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1456-1467
    • Belda, E.1    Moya, A.2    Silva, F.3
  • 3
    • 15344349176 scopus 로고    scopus 로고
    • On the properties of sequences of reversals that sort a signed permutation
    • Bergeron, A., Chauve, C., Hartman, T., et al. 2002. On the properties of sequences of reversals that sort a signed permutation. J. Biol. Inform. Math., 99-108.
    • (2002) J. Biol. Inform. Math , pp. 99-108
    • Bergeron, A.1    Chauve, C.2    Hartman, T.3
  • 4
    • 33846673442 scopus 로고    scopus 로고
    • Using median sets for inferring phylogenetic trees
    • Bernt M., Merkle, D., and Middendorf, M. 2007. Using median sets for inferring phylogenetic trees. Bioinformatics 23, 129-135.
    • (2007) Bioinformatics , vol.23 , pp. 129-135
    • Bernt, M.1    Merkle, D.2    Middendorf, M.3
  • 5
    • 46649120347 scopus 로고    scopus 로고
    • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    • Bhutkar, A., Gelbart, W., and Smith, T. 2007. Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. Genome Biol. 8, R236.
    • (2007) Genome Biol , vol.8
    • Bhutkar, A.1    Gelbart, W.2    Smith, T.3
  • 6
    • 0002163159 scopus 로고    scopus 로고
    • Breakpoint phylogenies
    • Miyano, S, and Takagi, T, eds, Universal Academy Press, Tokyo
    • Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies, 25-34. In Miyano, S., and Takagi, T., eds., Genome Informatics. Universal Academy Press, Tokyo.
    • (1997) Genome Informatics , pp. 25-34
    • Blanchette, M.1    Bourque, G.2    Sankoff, D.3
  • 7
    • 84947708594 scopus 로고    scopus 로고
    • The median problem for breakpoints in comparative genomics
    • Blanchette, M., and Sankoff, D. 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
    • Blanchette, M.1    Sankoff, D.2
  • 8
    • 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
  • 9
    • 34547488922 scopus 로고    scopus 로고
    • The solution space of sorting by reversals
    • Braga, M., Sagot, M., Scornavacca, C., et al. 2007. The solution space of sorting by reversals. Lect. Notes Bioinform. 4463, 293-304.
    • (2007) Lect. Notes Bioinform , vol.4463 , pp. 293-304
    • Braga, M.1    Sagot, M.2    Scornavacca, C.3
  • 10
    • 0032635206 scopus 로고    scopus 로고
    • Formulations and hardness of multiple sorting by reversals
    • Caprara, A. 1999a. Formulations and hardness of multiple sorting by reversals. RECOMB 1999 84-93.
    • (1999) RECOMB 1999 , pp. 84-93
    • Caprara, A.1
  • 11
    • 0002721941 scopus 로고    scopus 로고
    • Sorting permutations by reversals and Eulerian cycle decompositions
    • Caprara, A. 1999b. Sorting permutations by reversals and Eulerian cycle decompositions. SIAM J. Discrete Math. 12, 91-110.
    • (1999) SIAM J. Discrete Math , vol.12 , pp. 91-110
    • Caprara, A.1
  • 12
    • 84959064166 scopus 로고    scopus 로고
    • On the practical solution of the reversal median problem
    • Caprara, A. 2001. On the practical solution of the reversal median problem. Lect. Notes Comput. Sci. 2149, 238-251.
    • (2001) Lect. Notes Comput. Sci , vol.2149 , pp. 238-251
    • Caprara, A.1
  • 13
    • 0002110604 scopus 로고
    • Use of chloroplast DNA rearrangements in reconstructing plant phylogeny
    • Soltis, D, Soltis, P, and Doyle, J.J, eds, Chapman and Hall, New York
    • Downie, S.R., and Palmer, J.-D. 1992. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny, 14-35. In: Soltis, D., Soltis, P., and Doyle, J.J., eds. Molecular Systematics of Plants. Chapman and Hall, New York.
    • (1992) Molecular Systematics of Plants , pp. 14-35
    • Downie, S.R.1    Palmer, J.-D.2
  • 14
    • 33947374693 scopus 로고    scopus 로고
    • Reversal and transposition medians
    • Eriksen, N. 2007. Reversal and transposition medians. Theoret. Comput. Sci. 374, 111-126.
    • (2007) Theoret. Comput. Sci , vol.374 , pp. 111-126
    • Eriksen, N.1
  • 15
    • 0001807019 scopus 로고
    • Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
    • Hannenhalli, S., and Pevzner, P. 1995. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proc. 27th Annu. Symp. Theory Comput. 178-189.
    • (1995) Proc. 27th Annu. Symp. Theory Comput , pp. 178-189
    • Hannenhalli, S.1    Pevzner, P.2
  • 16
    • 84941152013 scopus 로고    scopus 로고
    • To cut . . . or not to cut (applications of comparative physical maps in molecular evolution)
    • Hannenhalli, S., and Pevzner, P. 1996. To cut . . . or not to cut (applications of comparative physical maps in molecular evolution). Proc. 7th ACM-SIAM Symp. Discrete Algorithms 304-313.
    • (1996) Proc. 7th ACM-SIAM Symp. Discrete Algorithms , pp. 304-313
    • Hannenhalli, S.1    Pevzner, P.2
  • 17
    • 84957042462 scopus 로고    scopus 로고
    • Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data
    • Moret, B., Siepel, A., Tang, J., et al. 2002. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Lect. Notes Comput. Sci. 2452, 521-536.
    • (2002) Lect. Notes Comput. Sci , vol.2452 , pp. 521-536
    • Moret, B.1    Siepel, A.2    Tang, J.3
  • 18
    • 19544394896 scopus 로고    scopus 로고
    • Reconstructing phylogenies from gene-content and gene-order data
    • Gascuel, O, ed, Oxford University Press, New York
    • Moret, B., Tang, J., and Warnow, T. 2005. Reconstructing phylogenies from gene-content and gene-order data, 321-352. In Gascuel, O., ed. Mathematics of Evolution and Phylogeny. Oxford University Press, New York.
    • (2005) Mathematics of Evolution and Phylogeny , pp. 321-352
    • Moret, B.1    Tang, J.2    Warnow, T.3
  • 19
    • 0035234694 scopus 로고    scopus 로고
    • A new implementation and detailed study of breakpoint analysis
    • Moret, B., Wyman, S., Bader, D., et al. 2001. A new implementation and detailed study of breakpoint analysis. Proc. 6th Pacif. Symp. Biocomput. 583-594.
    • (2001) Proc. 6th Pacif. Symp. Biocomput , pp. 583-594
    • Moret, B.1    Wyman, S.2    Bader, D.3
  • 20
    • 52449089795 scopus 로고    scopus 로고
    • Pe'er, I., and Shamir, R. 1998. The median problems for breakpoints are NP-complete. Elec. Colloq. Comput. Complexity 71.
    • Pe'er, I., and Shamir, R. 1998. The median problems for breakpoints are NP-complete. Elec. Colloq. Comput. Complexity 71.
  • 21
    • 0038271921 scopus 로고    scopus 로고
    • Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
    • Pevzner, P., and Tesler, G. 2003. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. Natl. Acad. Sci. USA 100, 7672-7677.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7672-7677
    • Pevzner, P.1    Tesler, G.2
  • 22
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D., and Foulds, L. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
    • (1981) Math. Biosci , vol.53 , pp. 131-147
    • Robinson, D.1    Foulds, L.2
  • 23
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 24
    • 0031721577 scopus 로고    scopus 로고
    • Multiple genome rearrangement and breakpoint phylogeny
    • Sankoff, D., and Blanchette, M. 1998. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 555-570.
    • (1998) J. Comput. Biol , vol.5 , pp. 555-570
    • Sankoff, D.1    Blanchette, M.2
  • 26
    • 0242690450 scopus 로고    scopus 로고
    • An algorithm to enumerate sorting reversals for signed permutations
    • Siepel, A. 2003. An algorithm to enumerate sorting reversals for signed permutations. J. Comput. Biol. 10, 575-597.
    • (2003) J. Comput. Biol , vol.10 , pp. 575-597
    • Siepel, A.1
  • 27
    • 84959066123 scopus 로고    scopus 로고
    • Finding an optimal inversion median: Experimental results
    • Siepel, A., and Moret, B. 2001. Finding an optimal inversion median: experimental results. Lect. Notes Comput. Sci. 2149, 189-203.
    • (2001) Lect. Notes Comput. Sci , vol.2149 , pp. 189-203
    • Siepel, A.1    Moret, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.