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192 results

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Page 1
Flow Sorting-Assisted Optical Mapping.
Šimková H, Tulpová Z, Cápal P. Šimková H, et al. Methods Mol Biol. 2023;2672:465-483. doi: 10.1007/978-1-0716-3226-0_28. Methods Mol Biol. 2023. PMID: 37335494
Optical mapping-a technique that visualizes short sequence motives along DNA molecules of hundred kilobases to megabase in size-has found an important place in genome research. ...Here, we provide a detailed protocol for the flow sorting-assisted uHMW DNA preparatio …
Optical mapping-a technique that visualizes short sequence motives along DNA molecules of hundred kilobases to megabase in siz …
Image processing for optical mapping.
Ravindran P, Gupta A. Ravindran P, et al. Gigascience. 2015 Nov 26;4:57. doi: 10.1186/s13742-015-0096-z. eCollection 2015. Gigascience. 2015. PMID: 26617984 Free PMC article. Review.
A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we de …
A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction …
Optical mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique.
Wang YK, Huff EJ, Schwartz DC. Wang YK, et al. Proc Natl Acad Sci U S A. 1995 Jan 3;92(1):165-9. doi: 10.1073/pnas.92.1.165. Proc Natl Acad Sci U S A. 1995. PMID: 7816810 Free PMC article.
We recently described a mapping technique, optical mapping, which uses fluorescence microscopy to produce high-resolution restriction maps rapidly by directly imaging restriction digestion cleavage events occurring on single deproteinized DNA mo …
We recently described a mapping technique, optical mapping, which uses fluorescence microscopy to produce high-resoluti …
Optical mapping of DNA: single-molecule-based methods for mapping genomes.
Neely RK, Deen J, Hofkens J. Neely RK, et al. Biopolymers. 2011 May;95(5):298-311. doi: 10.1002/bip.21579. Epub 2011 Jan 4. Biopolymers. 2011. PMID: 21207457 Review.
This review focuses on three enzymatic approaches to optical mapping. Optical mapping was first developed using restriction enzymes to sequence-specifically cleave DNA that is immobilized on a surface. More recently, nicking enzymes have found a …
This review focuses on three enzymatic approaches to optical mapping. Optical mapping was first developed using …
Optical mapping approaches to molecular genomics.
Schwartz DC, Samad A. Schwartz DC, et al. Curr Opin Biotechnol. 1997 Feb;8(1):70-4. doi: 10.1016/s0958-1669(97)80160-7. Curr Opin Biotechnol. 1997. PMID: 9013651 Free article. Review.
A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged site mapping, restriction enzyme fingerprinting, radiation hybrid mapping and optical mapping. ...
A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged si …
Determining optical mapping errors by simulations.
Vašinek M, Běhálek M, Gajdoš P, Fillerová R, Kriegová E. Vašinek M, et al. Bioinformatics. 2021 Oct 25;37(20):3391-3397. doi: 10.1093/bioinformatics/btab259. Bioinformatics. 2021. PMID: 33983386 Free article.
MOTIVATION: Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation sequencing (NGS). ...Optical mapping is affected by different kinds of errors in comparison with traditional DNA sequencing te …
MOTIVATION: Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation …
Computational methods for optical mapping.
Mendelowitz L, Pop M. Mendelowitz L, et al. Gigascience. 2014 Dec 30;3(1):33. doi: 10.1186/2047-217X-3-33. eCollection 2014. Gigascience. 2014. PMID: 25671093 Free PMC article. Review.
Optical mapping and newer genome mapping technologies based on nicking enzymes provide low resolution but long-range genomic information. ...Here, we review several algorithms and methods for building consensus optical maps and aligning restriction …
Optical mapping and newer genome mapping technologies based on nicking enzymes provide low resolution but long-range ge …
Signal-based optical map alignment.
Akdel M, van de Geest H, Schijlen E, van Rijswijck IMH, Smid EJ, Sanchez-Perez G, de Ridder D. Akdel M, et al. PLoS One. 2021 Sep 30;16(9):e0253102. doi: 10.1371/journal.pone.0253102. eCollection 2021. PLoS One. 2021. PMID: 34591846 Free PMC article.
In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optica …
In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and d …
Using optical mapping data for the improvement of vertebrate genome assemblies.
Howe K, Wood JM. Howe K, et al. Gigascience. 2015 Mar 18;4:10. doi: 10.1186/s13742-015-0052-y. eCollection 2015. Gigascience. 2015. PMID: 25789164 Free PMC article. Review.
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. ...In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference geno …
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction …
Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection.
Yuan Y. Yuan Y. Methods Mol Biol. 2022;2443:245-257. doi: 10.1007/978-1-0716-2067-0_13. Methods Mol Biol. 2022. PMID: 35037210
While DNA sequencing provides base-by-base nucleotide information, optical mapping shows the physical locations of selected enzyme restriction sites in a genome. ...Although optical mapping, therefore, offers unique advantages to researchers, th …
While DNA sequencing provides base-by-base nucleotide information, optical mapping shows the physical locations of selected en …
192 results