J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13 180-210, 1995.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....divided by total number of genes. While this approach does not work here due to the fact that all 20 mammalian mitochondrial genomes share exactly the same genes, notice the similarity of gene content formula and our general formula. Rearrangement Distance: Reversal and rearrangement distances in [18, 17, 27] compare genomes using other partial genome information such as number of reversals or translocations. These operations also do not appear in our mammalian mitochondrial genomes, hence the method again is not proper for our application. Transformation Distance or Compression Distance: The ....

J. Kececioglu and D. Sanko. Exact and approximation algorithms for the inversion distance. Algorithmica, 13(1995), 180-210.

....to compare genomes using gene order (Boore and Brown, 1998) and gene content(FitzGibbon and House, 1999; Snel et al. 1999) Such comparisons are time consuming as they require gene identi cation. These distances, together with G C content; edit distance; and reversal and rearrangement distances (Kececioglu and Sanko , 1995; Hannenhalli and Pevzner, 1995; Nadeau and Sanko , 1998) compare genomes using only partial genome information whereas our new distance uses all genome information. The transformation distance (Varre et al. 1998) and compression distance(Grumbach and Tahi, 1994) are essentially de ned as K(xjy) ....

Kececioglu, J. and Sanko, D. (1995). Exact and approximation algorithms for the inversion distance.

....this paradigm each motivated by a common type of genome rearrangement mechanism and indicate what is known about their respective diameter problems. One obtains the reversal distance between permutations by considering the set of all transformations that reverse a contiguous block of genes [1, 5, 6, 19]. Gollan conjectured that the diameter of the space of N element permutations under this distance function is N 1, and this was proved by Bafna and 2 Pevzner [1] One obtains the pre x reversal distance by considering the (smaller) set of all transformations that reverse a pre x of the ....

J. D. Kececioglu and D. Sanko. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13:180-210, 1995.

....paradigm each motivated by a common type of genome rearrangement mechanism and indicate what is known about their respective diameter problems. One obtains the reversal distance between permutations by considering the set of all transformations that reverse a contiguous block of genes [1, 5, 6, 19]. Gollan conjectured that the diameter of the space of N element permutations under this distance function is N 1, and this was proved by Bafna and 2 Pevzner [1] One obtains the prefix reversal distance by considering the (smaller) set of all transformations that reverse a prefix of the ....

J. D. Kececioglu and D. Sanko#. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13:180--210, 1995.

....identical or similar characters in both strings. Such alignments tend to reflect similar regions between the two strings that have remained conserved over the evolutionary process of point mutations that has led to the divergence between the two sequences. Recent studies on genome rearrangements [4,5,9,11,12,10] have addressed the notion of distances between sequences under more large scale mutational operations. An example is a reversal that works on a large contiguous block of a genomic sequence and reverses the order of certain markers in the fragment. Another macro mutational operation is a ....

J. Kececioglu and D. Sankoff, Exact and approximation algorithms for the inversion distance between two permutations, Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, pages 87--105. Springer Verlag, 1993.

....the order of an interval of genes. A shortest reversal sequence sorting one genome to another corresponds to the most likely evolutionary path between them. This analysis has been applied, for example, to drosophila [8, 21] plants [4, 18] viruses [12] and mammals [7, 20] Kececloglu and Sankoff [16] gave 2 approximation algorithms on reversal distance, which Bafna and Pevzner [3] improved to a factor of 7 4 approximation. Most recently, Hannenhalli and Pevzner [11] gave a polynomial time algorithm for signed reversal distance, although the problem for unsigned reversals (as we consider in ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, pages 87--105. Springer Verlag, 1993.

....in both strings. Such alignments tend to reflect similar regions between the two strings that have remained conserved over the evolutionary process of point mutations that has led to the divergence between the two sequences. 3 Recent studies on genome rearrangements [BP93, BP95, HP95, KS93, KS94, KR95] have addressed the notion of distances between sequences under more large scale mutational operations. An example is a reversal that works on a large contiguous block of a genomic sequence and reverses the order of certain markers in the fragment. Another macromutational ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, pages 87--105. Springer Verlag, 1993.

....the other species. The question of finding the reversal distance was first explored in the computer science context by Kececioglu and Sankoff and by Bafna and Pevzner and there has been significant progress made on this question by Bafna, Hannenhalli, Kececioglu, Pevzner, Ravi, Sankoff and others [1, 2, 7, 10, 11]. Other moves besides reversals have been considered as well. Breaking off a portion of the chromosome and inserting it elsewhere in the chromosome is referred to as a transposition and one can similarly define the transposition distance[3] Similarly allowing two chromosomes (viewed as strings of ....

J. Kececioglu and D. Sankoff. Exact and Approximation Algorithms for the Inversion Distance between Two Permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, Springer Verlag, 1993, pp. 87-105.

....esas areas relacionados con b usqueda aproximada no son s olo de la clase que hemos presentado. Por ejemplo, puede quererse buscar un patr on desconocido, del que s olo se conocen algunas propiedades. Se cree que incluso el problema simple es NP completo si se usan ciertas funciones de distancia [KS95, PW95] El lector interesado en obtener m as informaci on sobre el nacimiento de esta area puede consultar [SK83] En particular, Wat95, BSSU74, WL83, GK82, KG82] son buenas referencias para las aplicaciones de b usqueda aproximada en biolog ia computacional, as i como [DM79, Lev65, Vin68, ....

....to approximate searching are not only of the kind we have presented. For instance, one may look for an unknown pattern, of which only some properties are known. Even the simple problem of a known pattern is believed to be NP complete under some distance functions (e.g. sorting by reversals [KS95, PW95] We refer the reader interested in more information on the birth of this area to [SK83] In particular, good references for the applications of approximate pattern matching for computational biology are [Wat95, BSSU74, WL83, GK82, KG82] and for signal processing are [DM79, Lev65, Vin68, ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13:180--210, 1995.

....the other species. The question of finding the reversal distance was first explored in the computer science context by Kececioglu and Sankoff and by Bafna and Pevzner and there has been significant progress made on this question by Bafna, Hannenhalli, Kececioglu, Pevzner, Ravi, Sankoff and others [5, 6, 31, 45, 46]. Other moves besides reversals have been considered as well. Breaking off a portion of the chromosome and inserting it elsewhere in the chromosome is referred to as a transposition and one can similarly define the transposition distance[7] Similarly allowing two chromosomes (viewed as strings of ....

J. Kececioglu and D. Sankoff. Exact and Approximation Algorithms for the Inversion Distance between Two Permutations, Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, Springer Verlag, 1993, pp. 87-105.

....the other species. The question of finding the reversal distance was first explored in the computer science context by Kececioglu and Sankoff and by Bafna and Pevzner and there has been significant progress made on this question by Bafna, Hannenhalli, Kececioglu, Pevzner, Ravi, Sankoff and others [2, 3, 8, 11, 12, 13]. Other moves besides reversals have been considered as well. Breaking off a portion of the chromosome and inserting it elsewhere in the chromosome is referred to as a transposition and one can similarly define the transposition distance[4] Similarly allowing two chromosomes (viewed as strings of ....

J. Kececioglu and D. Sankoff. Exact and Approximation Algorithms for the Inversion Distance between Two Permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, Springer Verlag, 1993, pp. 87-105.

....2 through 4 have been compared to other heuristics by Johnson [7] and Bentley [1] and appear to be among the most effective TSP heuristics. For example, 3 Opt and Lin Kernighan return tours even better than simulated annealing 1 The same result was proved independently by Kececioglu and Sankoff [8] in the context of computing the number of chromosome inversions required to evolve one organism into another. 2 Note that our implementations of Fast 2 Opt and Fast 3 Opt differ slightly from Bentley s in that we precompute a nearest neighbor matrix of the 25 closest cities to each city in ....

J. Kececioglu and D. Sankoff, "Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes", in Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching, July 1993, pp. 87-105.

....order of an interval of genes. The minimum reversal sequence sorting the one genome to another corresponds to the most likely evolutionary path between them. This analysis has been applied, for example, to drosophila [9, 22] plants [5, 19] viruses [13] and man [8, 21] Kececloglu and Sankoff [17] gave 2 approximation algorithms on reversal distance, which Bafna and Pevzner [4] improved to a factor of 7 4 approximation. Most recently, Hannenhalli and Pevzner [12] gave a polynomial time algorithm for signed reversal distance, although the problem for unsigned reversals (as we consider in ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, pages 87--105. Springer Verlag, 1993.

....of gene intervals in related species (e.g. men and mice) may eliminate some of the ambiguities and lead to better estimates of gene locations. Although rearrangements of gene orders have been extensively studied in the computer science literature (see, for example, 1] 2] 3] 4] 5] [7], 8] 12] the problem of generating gene orders from experimental data remained largely unexplored. In particular, Hannenhalli and Pevzner [5] remarked that deriving gene orders is a non trivial task since the map 3 accuracy in human is significantly lower than in mouse, and for many closely ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13 180-210, 1995.

....based only on intrachromosomal events, such as inversion or transposition, can be defined for circular as well as linear chromosomes. An effort at a formalization of these processes in a common framework can be found in earlier papers [13, 14] Kececioglu and Sankoff [11] extended version of [8, 9]) considered the problem of computing the minimum reversal distance between two given permutations in the unsigned case, including approximation algorithms and an exact algorithm feasible for moderately long permutations. Bafna and Pevzner [1] gave improved approximation algorithms for this ....

J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two chromosomes. Proceedings of the 4th Symposium on Combinatorial Pattern Matching,Springer Verlag Lecture Notes in Computer Science 684:87-105, 1993.

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J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13 180-210, 1995.

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J. Kececioglu and D. Sanko#. Exact and approximation algorithms for the inversion distance. Algorithmica, 13(1995), 180210.

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J. Kececioglu and D. Sanko#. Exact and approximation algorithms for the inversion distance. Algorithmica, 13(1995), 180-210.

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J. Kececioglu and D. Sanko. Exact and approximation algorithms for the inversion distance between two permutations. In Proc. of 4th Ann. Symp. on Combinatorial Pattern Matching, Lecture Notes in Computer Science 684, pages 87-105. Springer Verlag, 1993.

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J. Kececioglu and D. Sankoff, Exact and approximation algorithms for the inversion distance between two permutations, Algorithmica 13:180-210, 1995.

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J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13 180-210, 1995.

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J. D. Kececioglu and D. Sanko#. Exact and approximation algorithms for the inversion distance between two permutations. Algorithmica, 13:180--210, 1995.

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