Hardness of flip-cut problems from optical mapping [DNA molecules application]

2002 ◽  
Author(s):  
V. Dancik ◽  
S. Hannenhalli ◽  
S. Muthukrishnan
Keyword(s):  
Optical Mapping ◽  
Dna Molecules ◽  
Cut Problems

scholarly journals Erratum: Corrigendum: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lena K. Nyberg ◽  
Saair Quaderi ◽  
Gustav Emilsson ◽  
Nahid Karami ◽  
Erik Lagerstedt ◽  
...  
Keyword(s):  
Bacterial Resistance ◽  
Optical Mapping ◽  
Rapid Identification ◽  
Dna Molecules ◽  
Single Dna Molecules ◽  
Resistance Plasmids

Molecular microscopy of DNA for genome analysis: optical mapping of restriction digests

1995 ◽  
Vol 53 ◽  
pp. 50-51
Author(s):  
Edward J. Huff ◽  
Weiwen Cai ◽  
Xinghua Hu ◽  
John Huang ◽  
Junping Jing ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Analysis ◽  
Optical Mapping ◽  
Ccd Camera ◽  
Dna Molecules ◽  
Specific Sequence ◽  
Single Dna Molecules ◽  
Single Clone ◽  
Rapid Generation ◽  
Glass Surfaces

Optical microscopy of individual DNA molecules has been an interesting technique for the past 15 years, but until recently has not been useful for genome analysis. We have developed Optical Mapping an emerging single molecule approach for the rapid generation of ordered restriction maps. Many identical individual DNA molecules from a single clone are elongated and fixed onto derivatized glass surfaces, digested with a restriction enzyme which cuts the DNA wherever a specific sequence pattern is found, stained with YOYO, and imaged with a cooled CCD camera attached to an automated epi-fluorescence microscope. Images are automatically processed to correct for non-uniform illumination, remove background, locate the DNA fragments, reject objects which do not look like single DNA molecules, recognize which fragments originate from an original uncut molecule, and calculate the relative sizes of the fragments by apparent length and fluorescence intensity. Results from many molecules are combined by clustering to recognize a consistent cutting pattern. Molecules which match the pattern are averaged to improve the sizing accuracy.

scholarly journals Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules

1998 ◽  
Vol 95 (14) ◽  
pp. 8046-8051 ◽  
Author(s):  
J. Jing ◽  
J. Reed ◽  
J. Huang ◽  
X. Hu ◽  
V. Clarke ◽  
...  
Keyword(s):  
High Resolution ◽  
Optical Mapping ◽  
Dna Molecules

scholarly journals Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Joanna M. Łopacińska-Jørgensen ◽  
Jonas N. Pedersen ◽  
Mads Bak ◽  
Mana M. Mehrjouy ◽  
Kristian T. Sørensen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Single Molecule ◽  
Optical Mapping ◽  
Next Generation ◽  
Dna Molecules ◽  
Generation Sequencing

scholarly journals Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

2021 ◽  
Vol 65 (1) ◽  
pp. 51-66 ◽  
Author(s):  
Jonathan Jeffet ◽  
Sapir Margalit ◽  
Yael Michaeli ◽  
Yuval Ebenstein
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Optical Mapping ◽  
Genome Mapping ◽  
Specific Cell ◽  
Dna Molecules ◽  
Genomic Information ◽  
Cell Functions ◽  
Fluorescent Tagging ◽  
Epigenetic Patterns

Abstract The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method’s basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method’s resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.

scholarly journals Optical Mapping of Plasmodium falciparum Chromosome 2

1999 ◽  
Vol 9 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Junping Jing ◽  
Zhongwu Lai ◽  
Christopher Aston ◽  
Jieyi Lin ◽  
Daniel J. Carucci ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
High Resolution ◽  
Genome Sequencing ◽  
Large Scale ◽  
Dna Analysis ◽  
Optical Mapping ◽  
Chromosome 2 ◽  
Dna Molecules ◽  
Restriction Maps ◽  
Plasmid Library

Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping withNheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.

Hardness of Flip-Cut Problems from Optical Mapping

1997 ◽  
Vol 4 (2) ◽  
pp. 119-125 ◽  
Author(s):  
VLADO DANČÍK ◽  
SRIDHAR HANNENHALLI ◽  
S. MUTHUKRISHNAN
Keyword(s):  
Optical Mapping ◽  
Cut Problems
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