Mass Estimation of DNA Molecules and Extraction of Ordered Restriction Maps in Optical Mapping Imagery

Algorithmica ◽  
1999 ◽  
Vol 25 (2-3) ◽  
pp. 295-310
Author(s):  
L. Parida ◽  
D. Geiger
Keyword(s):  
Optical Mapping ◽  
Dna Molecules ◽  
Restriction Maps ◽  
Mass Estimation

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.

Genomics via Optical Mapping II: Ordered Restriction Maps

1997 ◽  
Vol 4 (2) ◽  
pp. 91-118 ◽  
Author(s):  
THOMAS S. ANANTHARAMAN ◽  
BUD MISHRA ◽  
DAVID C. SCHWARTZ
Keyword(s):  
Optical Mapping ◽  
Restriction Maps

scholarly journals Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

2021 ◽  
Author(s):  
Kingshuk Mukherjee ◽  
Massimiliano Rossi ◽  
Daniel Dole-Muinos ◽  
Ayomide Ajayi ◽  
Mattia Prosperi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Optical Mapping ◽  
Gaussian Mixture ◽  
Restriction Maps ◽  
Entire Genome ◽  
Cpu Time ◽  
Genome Wide ◽  
Genomic Location ◽  
Optical Maps ◽  
Mixture Model Clustering

Optical mapping is a method for creating high resolution restriction maps of an entire genome. Optical mapping has been largely automated, and first produces single molecule restriction maps, called Rmaps, which are assembled to generate genome wide optical maps. Since the location and orientation of each Rmap is unknown, the first problem in the analysis of this data is finding related Rmaps, i.e., pairs of Rmaps that share the same orientation and have significant overlap in their genomic location. Although heuristics for identifying related Rmaps exist, they all require quantization of the data which leads to a loss in the precision. In this paper, we propose a Gaussian mixture modelling clustering based method, which we refer to as OMclust, that finds overlapping Rmaps without quantization. Using both simulated and real datasets, we show that OMclust substantially improves the precision (from 48.3% to 73.3%) over the state-of-the art methods while also reducing CPU time and memory consumption. Further, we integrated OMclust into the error correction methods (Elmeri and cOMet) to demonstrate the increase in the performance of these methods. When OMclust was combined with cOMet to error correct Rmap data generated from human DNA, it was able to error correct close to 3x more Rmaps, and reduced the CPU time by more than 35x. Our software is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/OMclust

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

2006 ◽  
Vol 103 (43) ◽  
pp. 15770-15775 ◽  
Author(s):  
A. Valouev ◽  
D. C. Schwartz ◽  
S. Zhou ◽  
M. S. Waterman
Keyword(s):  
Dna Molecules ◽  
Restriction Maps ◽  
Single Dna Molecules
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