On the complexity and approximation of syntenic distance

DasGupta, Bhaskar; Jiang, Tao; Kannan, Sampath; Li, M.; Sweedyk, Z.

doi:10.1145/267521.267536

Cited by 18 publications

(36 citation statements)

References 10 publications

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“…7. The reduction used two problems, the largest balanced quasi-independent set (LBQIS) problem and the largest balanced independent set (LBIS) problem.…”

Section: The Minimum Synteny Problemmentioning

confidence: 99%

“…Upon showing the NP-hardness of the Minimum Synteny problem, DasGupta et al presented an approximation algorithm for the problem with an approximation ratio of 2 7 . In computer science, approximation algorithms are algorithms used to find approximate solutions to optimization problems.…”

Section: The Minimum Synteny Problemmentioning

confidence: 99%

“…7. The total time needed to construct the synteny graph and find its connected components is O((4k + nk)A −1 (4k + nk, k)) = O(nkA −1 (nk, k)), where the function A −1 (x, y) is the inverse of the Ackermann function.…”

Section: {1 2 3}mentioning

confidence: 99%

“…Computing for the syntenic distance between genomes has already been proven to be an NP-Hard problem by DasGupta et al Furthermore, they provided a simple polynomial-time 2-approximation algorithm for it 7 .…”

Section: Introductionmentioning

confidence: 99%

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Polynomial-time Algorithm for Translocation Syntenic Distance

Belenzo¹,

Corpuz²,

Adorna³

et al. 2017

Theory and Practice of Computation

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Syntenic distance, an evolutionary distance model, is the minimum number of fusions, fissions, and translocations required to transform one genome into another. The problem of computing for the syntenic distance between two genomes has been proven to be NP-hard. Translocation syntenic distance is a special case of syntenic distance wherein operations are restricted to translocations. This restriction leads to the limitation of input instances to square instances only. As of writing, there remains no available computational complexity results for the problem of finding the minimum translocation syntenic distance between two genomes. In this paper, we focus on the translocation syntenic distance of square input instances with square connected components. A BFS-based polynomial-time algorithm for translocation syntenic distance is devised and proven effective. The algorithm runs on O(n 2 ) time and takes up O(n 2 ) space. A conjecture on the NP-hardness of the minimum translocation synteny problem is also presented. The idea behind the conjecture comes from the relationship between the translocation syntenic distance problem and the unsigned translocation distance problem, which was already proven to be NP-hard.

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“…7. The reduction used two problems, the largest balanced quasi-independent set (LBQIS) problem and the largest balanced independent set (LBIS) problem.…”

Section: The Minimum Synteny Problemmentioning

confidence: 99%

Section: The Minimum Synteny Problemmentioning

confidence: 99%

Section: {1 2 3}mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Polynomial-time Algorithm for Translocation Syntenic Distance

Belenzo¹,

Corpuz²,

Adorna³

et al. 2017

Theory and Practice of Computation

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“…Different metrics have been used to study secondary structures see [44] or biopolymer contact structures (see [45]). The interest in this domain as well as many important biological and medical implications of the study of genetic sequences is reflected on the number of several works performed (see for example [46][47][48][49][50][51]). …”

Section: Introductionmentioning

confidence: 99%

A Short Survey on Genetic Sequences, Chou’s Pseudo Amino Acid Composition and its Combination with Fuzzy Set Theory

Georgiou¹,

Karakasidis²,

Megaritis³

2013

TOBIOIJ

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Abstract:The study of genetic sequences is of great importance in biology and medicine. Sequence analysis and taxonomy are two major fields of application of bioinformatics. In this survey, we present results concerning genetic sequences and Chou's pseudo amino acid composition as well as methodologies developed based on this concept along with elements of fuzzy set theory, and emphasize on fuzzy clustering and its application in analysis of genetic sequences.

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