Exploring the Set of All Minimal Sequences of Reversals — An Application to Test the Replication-Directed Reversal Hypothesis

Ajana, Yasmine; Lefebvre, Jean‐François; Tillier, Elisabeth R. M.; El-Mabrouk, Nadia

doi:10.1007/3-540-45784-4_23

Cited by 35 publications

(47 citation statements)

References 11 publications

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“…In this example, [1,5] and [2,3] are conserved intervals, but not [1,6]. The other conserved intervals of P and Q are [1, -4], [1,8], [5, -4], [5,8] and [-4, 8].…”

Section: Conserved Intervalsmentioning

confidence: 94%

“…For example, the first four species of Table 1 share 6 adjacencies: [1,2], [2,3], [11,12], [15,16], [16,17], and [17,1]. When comparing all six species, the only left adjacency is [17,1]: this lack of conserved adjacencies is a direct consequence of how the data was transformed. Does this mean that losing common adjacencies amounts to losing all common structures?…”

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

“…For example, the genes between in the interval [1,12] are all the same, with small variations in their ordering. This is also true for the genes in the intervals: [3,6], [6,9], [9,11], and [12,17].…”

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

“…The right one uses much longer reversals than the left one, and the right one breaks conserved intervals between Silkworm and Locust in intermediate permutations, namely [3,6], [1,12], and [12,17]. If a rearrangement scenario is expected to reflect the various intermediate species between Silkworm and Locust, the right one looks highly suspicious.…”

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

“…The other conserved intervals of P and Q are [1, -4], [1,8], [5, -4], [5,8] and [-4, 8]. The diagram representation of these intervals, with respect to the permutation P , is:…”

Section: Conserved Intervalsmentioning

confidence: 99%

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On the Similarity of Sets of Permutations and Its Applications to Genome Comparison

Bergeron

Stoye

2003

Lecture Notes in Computer Science

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The comparison of genomes with the same gene content relies on our ability to compare permutations, either by measuring how much they differ, or by measuring how much they are alike. With the notable exception of the breakpoint distance, which is based on the concept of conserved adjacencies, measures of distance do not generalize easily to sets of more than two permutations. In this paper, we present a basic unifying notion, conserved intervals, as a powerful generalization of adjacencies, and as a key feature of genome rearrangement theories. We also show that sets of conserved intervals have elegant nesting and chaining properties that allow the development of compact graphic representations, and linear time algorithms to manipulate them.

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“…In this example, [1,5] and [2,3] are conserved intervals, but not [1,6]. The other conserved intervals of P and Q are [1, -4], [1,8], [5, -4], [5,8] and [-4, 8].…”

Section: Conserved Intervalsmentioning

confidence: 94%

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

Section: Permutations Gene Order and Rearrangementsmentioning

confidence: 99%

“…The other conserved intervals of P and Q are [1, -4], [1,8], [5, -4], [5,8] and [-4, 8]. The diagram representation of these intervals, with respect to the permutation P , is:…”

Section: Conserved Intervalsmentioning

confidence: 99%

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