Optical mapping in plant comparative genomics
Optical mapping has been widely used to improve de novo plant genome assemblies,
including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the …
including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the …
Computational methods for optical mapping
L Mendelowitz, M Pop - GigaScience, 2014 - academic.oup.com
Optical mapping and newer genome mapping technologies based on nicking enzymes
provide low resolution but long-range genomic information. The optical mapping technique …
provide low resolution but long-range genomic information. The optical mapping technique …
OMBlast: alignment tool for optical mapping using a seed-and-extend approach
Motivation Optical mapping is a technique for capturing fluorescent signal patterns of long
DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely …
DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely …
Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
The output from whole genome sequencing is a set of contigs, ie short non-overlapping DNA
sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult …
sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult …
Maligner: a fast ordered restriction map aligner
LM Mendelowitz, DC Schwartz, M Pop - Bioinformatics, 2016 - academic.oup.com
Abstract Motivation: The Optical Mapping System discovers structural variants and
potentiates sequence assembly of genomes via scaffolding and comparisons that globally …
potentiates sequence assembly of genomes via scaffolding and comparisons that globally …
OPTIMA: Sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis
Background Resolution of complex repeat structures and rearrangements in the assembly
and analysis of large eukaryotic genomes is often aided by a combination of high …
and analysis of large eukaryotic genomes is often aided by a combination of high …
Restriction Site Detection in Optical Mapping Data
Optical Mapping is a method of DNA sequencing that is used to detect large structural
variations in genomes. To create these optical maps a restriction enzyme is mixed with DNA …
variations in genomes. To create these optical maps a restriction enzyme is mixed with DNA …