Reconstruction of a String from Substring Precedence Data

Rubinov, Anatoly R.; Gelfand, Mikhail S.

doi:10.1089/cmb.1995.2.371

Cited by 5 publications

(3 citation statements)

References 12 publications

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“…In a string graph, the reconstructed genome can be modeled as a circular walk covering every node exactly once-Hamiltonian- [11,29], or at least once [27]. These models have also been considered in their weighted versions [21,27,29], or augmented to include other information, such as matepairs [33,23,14]. Each such notion of genomic reconstruction brought along questions concerning its validity.…”

Section: Related Workmentioning

confidence: 99%

Safe and Complete Contig Assembly Through Omnitigs

Tomescu

Medvedev

2017

Journal of Computational Biology

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Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs-a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question remains: given a genome graph G (e.g., a de Bruijn, or a string graph), what are all the strings that can be safely reported from G as contigs? In this article, we answer this question using a model in which the genome is a circular covering walk. We also give a polynomial-time algorithm to find such strings, which we call omnitigs. Our experiments show that omnitigs are 66%-82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.

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Section: Related Workmentioning

confidence: 99%

Safe and Complete Contig Assembly Through Omnitigs

Tomescu

Medvedev

2017

Journal of Computational Biology

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“…Specific details together with the classification of reconstruction ambiguities and the proof of the main algorithm validity are given in the accompanying paper (Rubinov and Gelfand, 1995).…”

Section: Algorithms and Methodsmentioning

confidence: 99%

Sequencing Potential of Nested Strand Hybridization

Razgulyaev¹,

Rubinov²,

Gelfand³

et al. 1995

Journal of Computational Biology

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The capability of the sequencing by nested strand hybridization (SNSH) method to sequence unseparated pools of DNA fragments was assessed in computer simulation experiments. The results demonstrate the high resolving power of the method and its tolerance to false-positive errors. We determine the optimal proportion between the fragment length and the pool size at a given length of oligonucleotide probes, compare SNSH to the standard SBH, and suggest the best experimental setting for the special case of sequencing of long isolated fragments.

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“…Similar string reconstruction problems have been considered in the past [ 6 , 7 ]. Rubinov and Gelfand [ 8 ] considered the problem of reconstructing a string given the set of k -long substrings and a list of all pairs of k -long subsequences ( i, j ) such that i precedes j at some distance in the string. Because they have complete, long-range precedence data, the problem is different than that which we consider here.…”

Section: Introductionmentioning

confidence: 99%

Assembly complexity of prokaryotic genomes using short reads

2010

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BackgroundDe Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes.ResultsWe provide the first survey of the repeat structure of a large number of genomes. The analysis gives an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths. Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. The non-reconstructible genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages).ConclusionsOur results improve upon previous studies on the feasibility of assembly with short reads and provide a comprehensive benchmark against which to compare the performance of the short-read assemblers currently being developed.

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Reconstruction of a String from Substring Precedence Data

Cited by 5 publications

References 12 publications

Safe and Complete Contig Assembly Through Omnitigs

Safe and Complete Contig Assembly Through Omnitigs

Sequencing Potential of Nested Strand Hybridization

Assembly complexity of prokaryotic genomes using short reads

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