Alignment of Optical Maps

Valouev, Anton; Li, Lei; Liu, Y. C.; Schwartz, David C.; Yang, Yi; Waterman, Michael S.

doi:10.1089/cmb.2006.13.442

Cited by 85 publications

(159 citation statements)

References 14 publications

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“…The sequences were then aligned (Valouev et al 2006) against the Nipponbare rice optical map (Zhou et al 2007) to automatically reveal any map-sequence discordances. The alignments were graphically viewed using GnomSpace (Teague et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Kawahara

Bastide

Hamilton

et al. 2013

Rice

1,814

1,610

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BackgroundRice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).ResultsThe Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.ConclusionsA revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Kawahara

Bastide

Hamilton

et al. 2013

Rice

1,814

1,610

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“…29 A pre-alignment filter step was applied requiring molecules to be greater than 50 kilobases and have a minimum of 5 labeled nick sites. The alignments of molecules whose p-value was less than 10 −4 were kept for further analysis.…”

Section: Methodsmentioning

confidence: 99%

Topological events in single molecules of E. coli DNA confined in nanochannels

Reifenberger

Dorfman

Cao

2015

Analyst

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We present experimental data concerning potential topological events such as folds, internal backfolds, and/or knots within long molecules of double-stranded DNA when they are stretched by confinement in a nanochannel. Genomic DNA from E. coli was labeled near the ‘GCTCTTC’ sequence with a fluorescently labeled dUTP analog and stained with the DNA intercalator YOYO. Individual long molecules of DNA were then linearized and imaged using methods based on the NanoChannel Array technology (Irys® System) available from BioNano Genomics. Data were collected on 189,153 molecules of length greater than 50 kilobases. A custom code was developed to search for abnormal intensity spikes in the YOYO backbone profile along the length of individual molecules. By correlating the YOYO intensity spikes with the aligned barcode pattern to the reference, we were able to correlate the bright intensity regions of YOYO with abnormal stretching in the molecule, which suggests these events were either a knot or a region of internal backfolding within the DNA. We interpret the results of our experiments involving molecules exceeding 50 kilobases in the context of existing simulation data for relatively short DNA, typically several kilobases. The frequency of these events is lower than the predictions from simulations, while the size of the events is larger than simulation predictions and often exceeds the molecular weight of the simulated molecules. We also identified DNA molecules that exhibit large, single folds as they enter the nanochannels. Overall, topological events occur at a low frequency (~7% of all molecules) and pose an easily surmountable obstacle for the practice of genome mapping in nanochannels.

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“…, where Y represents the true genomic size of corresponding region of DNA (17). This finding implies, for example, that for a 20-kb DNA fragment, 80% of the measurements are within 3.3 kb of 20 kb.…”

Section: Optical Mapping Measurementsmentioning

confidence: 94%

“…A directed overlap graph G ϭ (V, E) is defined by a set of nodes V corresponding to individual optical maps taken in a particular orientation, and a set of directed edges E, corresponding to high-quality overlaps between optical maps. Initially, all pairwise overlaps of optical maps are calculated by using our likelihood-based scoring method (17). The quality of reported overlaps is based on the site match measure that we term ''q score'' (A.V., unpublished data).…”

Section: Methodsmentioning

confidence: 99%

An algorithm for assembly of ordered restriction maps from single DNA molecules

Valouev

Schwartz²,

Zhou³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are ''in the noise'' or ''slightly above the noise.'' We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.whole-genome shotgun optical mapping ͉ map assembler

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Alignment of Optical Maps

Cited by 85 publications

References 14 publications

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Topological events in single molecules of E. coli DNA confined in nanochannels

An algorithm for assembly of ordered restriction maps from single DNA molecules

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