The Zero Exemplar Distance Problem

Jiang, Minghui

doi:10.1089/cmb.2011.0097

Cited by 20 publications

(11 citation statements)

References 16 publications

(24 reference statements)

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“…The exemplar genomic distance between G 1 and G 2 (loosely speaking, the 'true' distance when the redundant genes are deleted), while biologically interesting, is too hard to compute [12]. (In fact, unless P=NP, there does not exist any polynomial time approximation for such a distance even when each gene is allowed to repeat three times [5], [3] or even two times [1], [9].) We try to apply a different similarity measure here.…”

Section: Introductionmentioning

confidence: 99%

Scaffold Filling under the Breakpoint and Related Distances

Jiang¹,

Zheng

Sankoff

et al. 2012

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Abstract-Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, a problem on filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G was studied. The objective is to minimize the resulting genomic distance between I ′ and G, where I ′ is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we conduct a systematic study for the scaffold filling problem under the breakpoint distance and its variants, for both unichromosomal and multichromosomal genomes (with and without gene repetitions). 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 (i.e., G is also incomplete) is polynomially solvable for unichromosomal genomes under the breakpoint distance and for multichromosomal genomes under the genomic (or DCJ -Double-Cut-and-Join) distance. However, when the input genome contains some repeated genes, even the one-sided scaffold filling problem becomes NP-complete when the similarity measure is the maximum number of adjacencies between two sequences. For this problem, we also present efficient constant-factor approximation algorithms: factor-2 for the general case and factor 1.33 for the one-sided case.

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Section: Introductionmentioning

confidence: 99%

Scaffold Filling under the Breakpoint and Related Distances

Jiang¹,

Zheng

Sankoff

et al. 2012

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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“…When duplicate genes are present in the genomes, even finding minimum distances between two genomes is almost always an NP-Hard task [27]. In this paper, we focus on cherries of a species tree (i.e.…”

Section: Research Contextmentioning

confidence: 99%

Ancestral Genome Organization: An Alignment Approach

Holloway

Swenson

Ardell

et al. 2013

Journal of Computational Biology

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Abstract. We present a comparative genomics approach for inferring ancestral genome organization and evolutionary scenarios, based on present-day genomes represented as ordered gene sequences with duplicates. We develop our methodology for a model of evolution restricted to duplication and loss, and then show how to extend it to other content-modifying operations, and to inversions. From a combinatorial point of view, the main consequence of ignoring rearrangements is the possibility of formulating the problem as an alignment problem. On the other hand, duplications and losses are asymmetric operations that are applicable to one of the two aligned sequences. Consequently, an ancestral genome can directly be inferred from a duplication-loss scenario attached to a given alignment. Although alignments are a priori simpler to handle than rearrangements, we show that a direct approach based on dynamic programming leads, at best, to an efficient heuristic. We present an exact pseudo-boolean linear programming algorithm to search for the optimal alignment along with an optimal scenario of duplications and losses. Although exponential in the worst case, we show low running times on real datasets as well as synthetic data. We apply our algorithm 5 in a phylogenetic context to the evolution of stable RNA (tRNA and rRNA) gene content and organization in Bacillus genomes. Our results lead to various biological insights, such as rates of ribosomal RNA proliferation among lineages, their role in altering tRNA gene content, and evidence of tRNA class conversion.

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“…When duplicate genes are present in the genomes, even finding minimum distances between two genomes is almost always an NP-Hard task [19]. In this paper, we focus on cherries of a species tree (i.e.…”

Section: Research Contextmentioning

confidence: 99%

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach

Holloway

Swenson

Ardell

2012

Lecture Notes in Computer Science

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Abstract. We present a comparative genomics approach for inferring ancestral genome organization and evolutionary scenarios, based on a model accounting for content-modifying operations. More precisely, we focus on comparing two ordered gene sequences with duplicated genes that have evolved from a common ancestor through duplications and losses; our model can be grouped in the class of "Block Edit" models. From a combinatorial point of view, the main consequence is the possibility of formulating the problem as an alignment problem. On the other hand, in contrast to symmetrical metrics such as the inversion distance, duplications and losses are asymmetrical operations that are applicable to one of the two aligned sequences. Consequently, an ancestral genome can directly be inferred from a duplication-loss scenario attached to a given alignment. Although alignments are a priori simpler to handle than rearrangements, we show that a direct approach based on dynamic programming leads, at best, to an efficient heuristic. We present an exact pseudo-boolean linear programming algorithm to search for the optimal alignment along with an optimal scenario of duplications and losses. Although exponential in the worst case, we show low running times on real datasets as well as synthetic data. We apply our algorithm in a phylogenetic context to the evolution of stable RNA (tRNA and rRNA) gene content and organization in Bacillus genomes. Our results lead to various biological insights, such as rates of ribosomal RNA proliferation among lineages, their role in altering tRNA gene content, and evidence of tRNA class conversion.

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The Zero Exemplar Distance Problem

Cited by 20 publications

References 16 publications

Scaffold Filling under the Breakpoint and Related Distances

Scaffold Filling under the Breakpoint and Related Distances

Ancestral Genome Organization: An Alignment Approach

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach

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