Results 81 to 90 of about 1,350 (116)
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Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing, 1996Summary: Sequence comparison in molecular biology is in the beginning of a major paradigm shift -- a shift from gene comparison based on local mutations (i.e., insertions, deletions, and substitutions of nucleotides) to chromosome comparison based on global rearrangements (i.e., inversions and transpositions of fragments).
Pavel Pevzner, Vineet Bafna
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On the Complexity of Sorting by Reversals and Transpositions Problems
Journal of Computational Biology, 2019Abstract In comparative genomics, rearrangements are mutations that affect a stretch of DNA sequences. Reversals and transpositions are well-known rearrangements, and each has a vast literature.
K L Brito +2 more
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Sorting Signed Permutations by Intergenic Reversals
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021Genome rearrangements are mutations affecting large portions of a genome, and a reversal is one of the most studied genome rearrangements in the literature through the Sorting by Reversals (SbR) problem. SbR is solvable in polynomial time on signed permutations (i.e., the gene orientation is known), and it is NP-hard on unsigned permutations.
K L Brito +2 more
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An Algorithm to Enumerate Sorting Reversals for Signed Permutations
Journal of Computational Biology, 2003The rearrangement distance between single-chromosome genomes can be estimated as the minimum number of inversions required to transform the gene ordering observed in one into that observed in the other. This measure, known as "inversion distance," can be computed as the reversal distance between signed permutations.
Adam Siepel
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1996
Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n4) implementation of the algorithm.
Piotr Berman, Sridhar Hannenhalli
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Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n4) implementation of the algorithm.
Piotr Berman, Sridhar Hannenhalli
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Sorting by Weighted Reversals and Transpositions
Journal of Computational Biology, 2018Abstract Genome rearrangements are global mutations that change large stretches of DNA sequence throughout genomes. They are rare but accumulate during the evolutionary process leading to organisms with similar genetic material in different places and orientations within the genome.
Andre Rodrigues Oliveira +3 more
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Sorting by Block-Interchanges and Signed Reversals
Fourth International Conference on Information Technology (ITNG'07), 2007A block-interchange is a rearrangement event that exchanges two, not necessarily consecutive, contiguous regions in a genome, maintaining the original orientation. Signed reversals are events that invert and change the orientation of a region in a genome. Both events are important for the comparative analysis of genomes.
Cleber V. G. Mira, Joao Meidanis
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Sorting by Reversals with Common Intervals
2004Studying rearrangements from gene order data is a standard approach in evolutionary analysis. Gene order data are usually modeled as signed permutations. The computation of the minimal number of reversals between two signed permutations produced a lot of literature during the last decade.
Martin Figeac, Jean-Stéphane Varré
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An algorithm for sorting pancake by restricted reversals
The Journal of Supercomputing, 2015In this paper, we propose an algorithm for sorting n pancakes. The previous studies were focused on finding upper bound or lower bound regarding a limited n-pancake. This study, however, suggests the algorithms for n-pancake with $$n\ge 5$$n?5. The only constraint is that $$n\ge 5$$n?5, which eliminates the very strong constraints [$$n\equiv 0$$n?0 ...
JungHyun Seo +2 more
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Sorting by Reversals and Transpositions with Proportion Restriction
2020In the field of comparative genomics, one way of comparing two genomes is through the analysis of how they distinguish themselves based on a set of mutations called rearrangement events. When considering that genomes undergo different types of rearrangements, it can be assumed that some events are more common than others.
Klairton Lima Brito +4 more
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