The greedy algorithm for the minimum common string partition problem

Chrobák, Marek; Kolman, Petr; Sgall, Jiřį́

doi:10.1145/1103963.1103971

Cited by 36 publications

(32 citation statements)

References 12 publications

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“…The NP-hardness holds even if the instance is restricted to have multiplicity at most k, i.e., an instance of k-MCSP, for any k 2. Approximation algorithms for MCSP have been recently investigated in [9,[44][45][46]. In particular, [9] presents an approximation algorithm based on a new graphical structure called pair-match graphs.…”

Section: Minimum Common Substring Partitionmentioning

confidence: 99%

Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

Jiang

2010

J. Comput. Sci. Technol.

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Genome-scale assignment of orthologous genes is a fundamental and challenging problem in computational biology and has a wide range of applications in comparative genomics, functional genomics, and systems biology. Many methods based on sequence similarity, phylogenetic analysis, chromosomal syntenic information, and genome rearrangement have been proposed in recent years for ortholog assignment. Although these methods produce results that largely agree with each other, their results may still contain significant differences. In this article, we consider the recently proposed parsimony approach for assigning orthologs between closely related genomes based on genome rearrangement, which essentially attempts to transform one genome into another by the smallest number of genome rearrangement events including reversal, translocation, fusion, and fission, as well as gene duplication events. We will highlight some of the challenging algorithmic problems that arise in the approach including (i) minimum common substring partition, (ii) signed reversal distance with duplicates, and (iii) signed transposition distance with duplicates. The most recent progress towards the solution of these problems will be reviewed and some open questions will be posed. We will also discuss some possible extensions of the approach to the simultaneous comparison of multiple genomes.

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Section: Minimum Common Substring Partitionmentioning

confidence: 99%

Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

Jiang

2010

J. Comput. Sci. Technol.

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“…Choosing an optimal set of strings c j might be intractable, since even if the strings are restricted to be the prefixes or suffixes of words in the text, the problem of finding the set is NP-complete [7], and other similar problems of devising a code have also been shown to be NP-complete in [5,10,6]. A natural approach is thus to suggest heuristical solutions and compare their efficiencies.…”

Section: Introductionmentioning

confidence: 99%

On improving Tunstall codes

Klein

Shapira

2011

Information Processing & Management

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Abstract. Though many compression methods are based on the use of variable length codes, there has recently been a trend to search for alternatives in which the lengths of the codewords are more restricted, which can be useful for fast decoding and compressed searches. This paper explores the construction of variable-to-fixed length codes, which have been suggested long ago by Tunstall. Using new heuristics based on suffix trees, the performance of Tunstall codes can in some cases be improved by more than 40%.

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“…However, when the input genome contains some genes which appear twice, even the one-sided scaffold filling problem becomes NP-complete. The latter problem has a close connection with the Minimum Common String Partition (MCSP) problem [2,3,4,7,8,9]. This paper is organized as follows.…”

Section: Introductionmentioning

confidence: 99%

Scaffold Filling under the Breakpoint Distance

Jiang

Zheng

Sankoff

et al. 2010

Comparative Genomics

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Abstract.Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, Muñoz et al. recently studied the problem of filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G such that the resulting genomic distance between I and G is minimized, where I is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we follow Muñoz et al. to investigate the scaffold filling problem under the breakpoint distance for the simplest unichromosomal genomes. When the input genome contains no gene repetition (i.e., is a fragment of a permutation), we show that the two-sided scaffold filling problem is polynomially solvable. However, when the input genome contains some genes which appear twice, even the one-sided scaffold filling problem becomes NP-complete. Finally, using the ideas for solving the two-sided scaffold filling problem under the breakpoint distance we show that the two-sided scaffold filling problem under the genomic/rearrangement distance is also polynomially solvable.

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The greedy algorithm for the minimum common string partition problem

Cited by 36 publications

References 12 publications

Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

On improving Tunstall codes

Scaffold Filling under the Breakpoint Distance

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