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 Experiment Videos

AMASS: a structured pattern matching approach to shotgun sequence assembly.

S Kim1, A M Segre

  • 1Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, USA. sunkim@micro5.es.dupont.com

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|July 27, 1999
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Testing Optical Character Recognition of Home Blood Pressure Measurements, a Randomized Trial.

American journal of hypertension·2025
Same author

Intracerebral infusion of thrombin as a cause of brain edema.

Journal of neurosurgery·1995
Same author

Human T-lymphotropic virus type 1 in coastal natives of British Columbia: phylogenetic affinities and possible origins.

Journal of virology·1995
Same author

Leptin levels in human and rodent: measurement of plasma leptin and ob RNA in obese and weight-reduced subjects.

Nature medicine·1995
Same author

Crystal structure of a complement factor D mutant expressing enhanced catalytic activity.

The Journal of biological chemistry·1995
Same author

Blockage of the early events of mitogenic signaling by interferon-gamma in macrophages in response to colony-stimulating factor-1.

Blood·1995

This study introduces a fast and reliable shotgun sequencing algorithm using fingerprinting to overcome noise and repetitive DNA challenges. The method accurately assembles genomes, significantly outperforming existing approaches in speed and robustness.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Whole-genome shotgun sequencing is crucial for genomic research.
  • Noise and repetitive sequences present significant challenges for accurate genome assembly.
  • Existing assembly algorithms often struggle with data complexity and speed.

Purpose of the Study:

  • To develop an efficient and reliable shotgun sequence assembly algorithm.
  • To address the limitations of existing methods in handling noisy and repetitive DNA data.
  • To improve the speed and accuracy of whole-genome shotgun sequencing.

Main Methods:

  • Utilizes a fingerprinting scheme based on exact matches of short, randomly selected patterns from fragment data.
  • Identifies fragment overlaps and constructs an overlap map.

Related Experiment Videos

  • Employs statistical clues to manage repetitive sequences and data noise.

    • Main Results:

    • Successfully assembled the Mycoplasma genitalium genome (580 kbp) in approximately 8 minutes.
    • Demonstrated robustness and accuracy on artificially shotgunned human DNA (238 kbp) in under 3 minutes.
    • Achieved significantly faster assembly times compared to existing algorithms, which typically require hours to days.

    Conclusions:

    • The proposed fingerprinting-based algorithm offers a highly efficient and accurate solution for shotgun sequence assembly.
    • The method effectively overcomes common challenges posed by noise and repetitive sequences in genomic data.
    • This approach represents a substantial advancement in the speed and reliability of whole-genome sequencing and assembly.