Abstract
The syntenic distance between two genomes is the minimum number of fusions, fissions, and translocations that can transform one genome to the other, ignoring the gene order within chromosomes. As the problem is NP-hard in general, some particular classes of synteny instances, such as linear synteny, exact synteny and nested synteny, are examined in the literature. In this paper, we propose a new special class of synteny instances, called uncovering synteny. We first present a polynomial time algorithm to solve the connected case of uncovering synteny optimally. By performing only intra-component moves, we then solve the unconnected case of uncovering synteny. We will further calculate the diameters of connected and unconnected uncovering synteny, respectively.
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References
Bafna V, Pevzner P (1996) Genome rearrangements and sorting by reversals. SIAM J Comput 25(2):272–289
Bafna V, Pevzner P (1998) Sorting by transpositions. SIAM J Disc Math 11(2):224–240
Caprara A (1997) Sorting by reversals is difficult. In: Proceedings of the 1st ACM int conf comput mole biol, pp 75–83
Chauve C, Fertin G (2004) On maximal instances for the original syntenic distance. Theor Comp Sci 326:29–43
Christie DA (1999) Genome rearrangement problems. Ph.D. dissertation, University of Glasgow
DasGupta B, Jiang T, Kannan S, Li M, Sweedyk E (1998) On the complexity and approximation of syntenic distance. Discr Appl Math (special issue in computational biology) 88(1–3):59–82
Ferretti V, Nadeau JH, Sankoff D (1996) Original synteny. In: CPM 1996, Lecture notes in computer science, Springer-Verlag, Berlin, Vol 1075, pp 159–167
Gu QP, Peng S, Sudborough H (1999) A 2-approximation algorithm for genome rearrangements by reversals and transpositions. Theor Comp Sci 210:327–339
Hannenhalli S, Pevzner P (1995) Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Proceedings of the 27th ACM symposium on theory of computing, pp 178–189
Kececioglu J, Sankoff D (1993) Exact and approximation algorithms for the inversion distance between two permutations. In: CPM: 1993, Lecture notes in computer science, Springer-Verlag, Berlin, Vol 687, pp 87–105
Kececioglu J, Sankoff D (1994) Efficient bounds for oriented chromosome inversion distance. In: CPM 1994, Lecture notes in computer science, Springer-Verlag, Berlin, Vol. 807, pp 307–325
Kececioglu J, Sankoff D (1995) Exact and approximation algorithms for sorting by reversals, with application to genome rearrangements. Algorithmica 13:180–210
Kleinberg J, Liben-Nowell D (2000) The syntenic diameter of the space of N-chromosome genomes. In: Proceedings of the conference on gene order dynamics, comparative maps, and multigene families (DCAF), pp 185–197
Liben-Nowell D (1999) On the structure of syntenic distance. In: CPM 1999, Lecture notes in computer science, Springer-Verlag, Berlin, Vol. 1645, pp. 50–65
Liben-Nowell D (2002) Gossip is synteny: incomplete gossip and syntenic distance between genomes. J Algorith 43(2):264–283
Liben-Nowell D, Kleinberg J (2000) Structural properties and tractability results for linear synteny. In: CPM 2000, Lecture notes in computer science, Springer-Verlag, Berlin, Vol. 1848, pp. 248–263
Lin G-H, Xue G-L (2001) Signed genome rearrangement by reversals and transpositions: models and approximations. Theor Comp Sci 259(1–2):513–531
Pisanti N, Sagot MF (2002) Further thoughts on the syntenic distance between genomes. Algorithmica 34:157–180
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Ting, C., Yong, H.E. Optimal algorithms for uncovering synteny problem. J Comb Optim 12, 421–432 (2006). https://doi.org/10.1007/s10878-006-9008-6
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DOI: https://doi.org/10.1007/s10878-006-9008-6