메뉴 건너뛰기




Volumn 4751 LNBI, Issue , 2007, Pages 30-44

Improving inversion median computation using commuting reversals and cycle information

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATION THEORY; DATA REDUCTION; DATA STRUCTURES; OPTIMIZATION; PROBLEM SOLVING;

EID: 38349003267     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74960-8_3     Document Type: Conference Paper
Times cited : (6)

References (26)
  • 1
    • 0034767147 scopus 로고    scopus 로고
    • A fast linear-time algorithm for inversion distance with an experimental comparison
    • Bader, D.A., Moret, B.M.E., Yan, M.: A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8(5), 483-491 (2001)
    • (2001) J. Comput. Biol , vol.8 , Issue.5 , pp. 483-491
    • Bader, D.A.1    Moret, B.M.E.2    Yan, M.3
  • 2
    • 33747398328 scopus 로고    scopus 로고
    • Bernt, M., Merkle, D., Middendorf, M.: Genome rearrangement based on reversals that preserve conserved intervals. IEEE/ACM Trans. on Comput. Biol, and Bioinfo. 3(3), 275-288 (2006)
    • Bernt, M., Merkle, D., Middendorf, M.: Genome rearrangement based on reversals that preserve conserved intervals. IEEE/ACM Trans. on Comput. Biol, and Bioinfo. 3(3), 275-288 (2006)
  • 3
    • 33846673442 scopus 로고    scopus 로고
    • Using median sets for inferring phylogenetic trees
    • Bernt, M., Merkle, D., Middendorf, M.: Using median sets for inferring phylogenetic trees. Bioinformatics 23(2), 129-135 (2007)
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 129-135
    • Bernt, M.1    Merkle, D.2    Middendorf, M.3
  • 4
    • 84947708594 scopus 로고    scopus 로고
    • The median problem for breakpoints in comparative genomics
    • Jiang, T, Lee, D.T, eds, COCOON 1997, Springer, Heidelberg
    • Blanchette, M., Sankoff, D.: The median problem for breakpoints in comparative genomics. In: Jiang, T., Lee, D.T. (eds.) COCOON 1997. LNCS, vol. 1276, pp. 251-263. Springer, Heidelberg (1997)
    • (1997) LNCS , vol.1276 , pp. 251-263
    • Blanchette, M.1    Sankoff, D.2
  • 5
    • 0002163159 scopus 로고    scopus 로고
    • Breakpoint phylogenies
    • Miyano, S, Takagi, T, eds, Univ. Academy Press
    • Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. In: Miyano, S., Takagi, T. (eds.) Genome Informatics, pp. 25-34. Univ. Academy Press (1997)
    • (1997) Genome Informatics , pp. 25-34
    • Blanchette, M.1    Bourque, G.2    Sankoff, D.3
  • 6
    • 38349011830 scopus 로고    scopus 로고
    • Bergeron, A., Chauve, C., Hartman, T., St-Onge, K.: On the Properties of Sequences of Reversals that Sort a Signed Permutation. Journal Ouvertes Biologie, Informatique, Mathematiques (JOBIM 2002), 99-108 (2002)
    • Bergeron, A., Chauve, C., Hartman, T., St-Onge, K.: On the Properties of Sequences of Reversals that Sort a Signed Permutation. Journal Ouvertes Biologie, Informatique, Mathematiques (JOBIM 2002), 99-108 (2002)
  • 7
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque, G., Pevzner, P.: Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Research 12, 26-36 (2002)
    • (2002) Genome Research , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.2
  • 8
    • 0032635206 scopus 로고    scopus 로고
    • Formulations and hardness of multiple sorting by reversals
    • ACM Press, New York
    • Caprara, A.: Formulations and hardness of multiple sorting by reversals. In: Proc. 3rd Int'l Conf. on Comput. Mol. Biol. RECOMB99, pp. 84-93. ACM Press, New York (1999)
    • (1999) Proc. 3rd Int'l Conf. on Comput. Mol. Biol. RECOMB99 , pp. 84-93
    • Caprara, A.1
  • 9
    • 0002721941 scopus 로고    scopus 로고
    • Sorting permutations by reversals and Eulerian cycle decompositions
    • Caprara, A.: Sorting permutations by reversals and Eulerian cycle decompositions. SIAM J. Discrete Math. 12(1), 91-110 (1999)
    • (1999) SIAM J. Discrete Math , vol.12 , Issue.1 , pp. 91-110
    • Caprara, A.1
  • 10
    • 84959064166 scopus 로고    scopus 로고
    • Caprara, A.: On the practical solution of the reversal median problem. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, 2149, pp. 238-251. Springer, Heidelberg (2001)
    • Caprara, A.: On the practical solution of the reversal median problem. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 238-251. Springer, Heidelberg (2001)
  • 11
    • 0002110604 scopus 로고
    • Use of chloroplast DNA rearrangements in reconstructing plant phylogeny
    • Soltis, P, et al, eds
    • Downie, S., Palmer, J.: Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis, P., et al. (eds.) Plant Molecular Systematics, pp. 14-35 (1992)
    • (1992) Plant Molecular Systematics , pp. 14-35
    • Downie, S.1    Palmer, J.2
  • 12
    • 33947374693 scopus 로고    scopus 로고
    • Reversal and Transposition Medians. Theoretical Computer
    • Eriksen, N.: Reversal and Transposition Medians. Theoretical Computer Sicence 374, 111-126 (2007)
    • (2007) Sicence , vol.374 , pp. 111-126
    • Eriksen, N.1
  • 13
    • 0001807019 scopus 로고
    • Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
    • ACM Press, New York
    • Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Proc. 27th Ann. Symp. Theory of Computing STOC'95, pp. 178-189. ACM Press, New York (1995)
    • (1995) Proc. 27th Ann. Symp. Theory of Computing STOC'95 , pp. 178-189
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 14
    • 84941152013 scopus 로고    scopus 로고
    • To cut... or not to cut (applications of comparative physical maps in molecular evolution)
    • SIAM Press
    • Hannenhalli, S., Pevzner, P.A.: To cut... or not to cut (applications of comparative physical maps in molecular evolution). In: Proc. 7th ACM-SIAM Symp. on Discrete Algorithms (SODA'96), pp. 304-313. SIAM Press (1996)
    • (1996) Proc. 7th ACM-SIAM Symp. on Discrete Algorithms (SODA'96) , pp. 304-313
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 15
    • 14544300681 scopus 로고    scopus 로고
    • A Bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol, and Evol
    • Larget, B., Simon, D.L., Kadane, J.B., Sweet, D.: A Bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol, and Evol. 22(3), 486-495 (2005)
    • (2005) , vol.22 , Issue.3 , pp. 486-495
    • Larget, B.1    Simon, D.L.2    Kadane, J.B.3    Sweet, D.4
  • 16
    • 84957042462 scopus 로고    scopus 로고
    • Moret, B.M.E., Siepel, A., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, 2452, pp. 521-536. Springer, Heidelberg (2002)
    • Moret, B.M.E., Siepel, A., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 521-536. Springer, Heidelberg (2002)
  • 18
    • 19544394896 scopus 로고    scopus 로고
    • Reconstructing phylogenies from gene-content and gene-order data
    • Gascuel, O, ed, Oxford Univ. Press, Oxford, UK
    • Moret, B.M.E., Tang, J., Warnow, T.: Reconstructing phylogenies from gene-content and gene-order data. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny, pp. 321-352. Oxford Univ. Press, Oxford, UK (2005)
    • (2005) Mathematics of Evolution and Phylogeny , pp. 321-352
    • Moret, B.M.E.1    Tang, J.2    Warnow, T.3
  • 19
    • 0002880994 scopus 로고
    • Chloroplast and mitochondria genome evolution in land plants
    • Herrmann, R, ed
    • Palmer, J.: Chloroplast and mitochondria genome evolution in land plants. In: Herrmann, R. (ed.) Cell Organelles, pp. 99-133 (1992)
    • (1992) Cell Organelles , pp. 99-133
    • Palmer, J.1
  • 20
    • 37149001085 scopus 로고    scopus 로고
    • The median problems for breakpoints are NP-complete. Elec. Colloq. on Comput
    • Pe'er, I., Shamir, R.: The median problems for breakpoints are NP-complete. Elec. Colloq. on Comput. Complexity 71 (1998)
    • (1998) Complexity , vol.71
    • Pe'er, I.1    Shamir, R.2
  • 21
    • 0038271921 scopus 로고    scopus 로고
    • Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
    • Pevzner, P., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. of Natl. Acad. of Sci. USA 100, 7672-7677 (2003)
    • (2003) Proc. of Natl. Acad. of Sci. USA , vol.100 , pp. 7672-7677
    • Pevzner, P.1    Tesler, G.2
  • 22
    • 0026598577 scopus 로고
    • Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants
    • Raubeson, L., Jansen, R.: Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255, 1697-1699 (1992)
    • (1992) Science , vol.255 , pp. 1697-1699
    • Raubeson, L.1    Jansen, R.2
  • 23
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987)
    • (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., Blanchette, M.: Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 555-570 (1998)
    • (1998) J. Comput. Biol , vol.5 , pp. 555-570
    • Sankoff, D.1    Blanchette, M.2
  • 25
    • 84959066123 scopus 로고    scopus 로고
    • Siepel, A., Moret, B.M.E.: Finding an optimal inversion median: experimental results. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, 2149, pp. 189-203. Springer, Heidelberg (2001)
    • Siepel, A., Moret, B.M.E.: Finding an optimal inversion median: experimental results. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 189-203. Springer, Heidelberg (2001)
  • 26
    • 0242690450 scopus 로고    scopus 로고
    • An algorithm to enumerate sorting reversals for signed permutations
    • Siepel, A.: An algorithm to enumerate sorting reversals for signed permutations. J. Comput. Biol. 10, 575-597 (2003)
    • (2003) J. Comput. Biol , vol.10 , pp. 575-597
    • Siepel, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.