Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Distance Measurements by Taping01:18

Distance Measurements by Taping

187
Tapes are essential in surveying for accurate, durable, and short-distance measurements. Made from lightweight, nylon-coated steel, they offer flexibility and strength for rugged outdoor use. The nylon coating protects against rust and wear, extending the tape's life. Standard lengths, around 30 meters, are marked in meters and millimeters for precision.Surveyors select tapes based on site conditions and accuracy needs. Lightweight, nylon-coated tapes are commonly used for ease of handling and...
187
Distance Corrections01:15

Distance Corrections

132
To achieve precise distance measurements, especially in surveying and construction, certain corrections must be applied to account for potential sources of error like the standardization errors, temperature variations, and slope adjustments.Standardization error emerges when measurement equipment undergoes changes, such as wear, repairs, or weather impacts. To address this, surveyors compare the equipment’s readings to a standard. This process identifies any deviation that might lead to...
132

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.

Bioinformatics (Oxford, England)·2026
Same author

DipSkmer: Reference-free population genomics with diploid genome skims.

bioRxiv : the preprint server for biology·2026
Same author

Preservation and clonal behavior of extrachromosomal DNA in patient-derived xenograft models of childhood cancers.

Genome medicine·2026
Same author

ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.

Genome biology·2026
Same author

High-depth whole genome sequencing of premalignant breast lesions reveals rearrangement hotspots and personalized management opportunities.

Nature communications·2026
Same author

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Nov 4, 2025

High-Throughput Analysis of Optical Mapping Data Using ElectroMap
07:36

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

Published on: June 4, 2019

9.7K

FaNDOM: Fast nested distance-based seeding of optical maps.

Siavash Raeisi Dehkordi1, Jens Luebeck1,2, Vineet Bafna1

  • 1Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA.

Patterns (New York, N.Y.)
|May 24, 2021
PubMed
Summary

FaNDOM, a new optical map alignment tool, significantly speeds up the identification of genomic structural variants. This advancement aids in discovering biologically relevant rearrangements in cancer cell lines.

Keywords:
DSML 3: Development/Pre-production: Data science output has been rolled out/validated across multiple domains/problems

More Related Videos

Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping
09:43

Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping

Published on: March 20, 2017

10.1K
Determining 3D Flow Fields via Multi-camera Light Field Imaging
14:25

Determining 3D Flow Fields via Multi-camera Light Field Imaging

Published on: March 6, 2013

16.8K

Related Experiment Videos

Last Updated: Nov 4, 2025

High-Throughput Analysis of Optical Mapping Data Using ElectroMap
07:36

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

Published on: June 4, 2019

9.7K
Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping
09:43

Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping

Published on: March 20, 2017

10.1K
Determining 3D Flow Fields via Multi-camera Light Field Imaging
14:25

Determining 3D Flow Fields via Multi-camera Light Field Imaging

Published on: March 6, 2013

16.8K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Optical mapping (OM) offers single-molecule DNA analysis at nucleotide resolution.
  • Microfluidic technologies enable cost-effective generation of long OM data.
  • OM data aids in genome scaffolding and structural variant identification.

Purpose of the Study:

  • Introduce FaNDOM (Fast Nested Distance Seeding of Optical Maps), an efficient optical map alignment tool.
  • Improve the speed and scalability of structural variant detection using optical maps.
  • Apply FaNDOM to identify structural variants in cancer cell lines.

Main Methods:

  • Developed FaNDOM, a novel algorithm for optical map alignment.
  • Utilized microfluidic technologies for generating long optical map data.
  • Benchmarked FaNDOM against existing tools on human datasets.

Main Results:

  • FaNDOM demonstrated 4-14× speed improvement over competing tools.
  • Maintained comparable sensitivity and specificity in structural variant detection.
  • Identified numerous biologically relevant structural variants in three cancer cell lines, including deletions, duplications, and gene fusions.

Conclusions:

  • FaNDOM significantly accelerates optical map alignment and structural variant discovery.
  • The tool facilitates the identification of complex genomic rearrangements in cancer.
  • FaNDOM is publicly available, promoting broader adoption in genomic research.