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

Sequence alignment by cross-correlation.

Alan L Rockwood1, David K Crockett, James R Oliphant

  • 1ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA. rockwoal@aruplab.com

Journal of Biomolecular Techniques : JBT
|March 9, 2006
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

Familial clustering and physiological risk factors associated with intervertebral disc degeneration in a large population-based cohort.

Osteoarthritis and cartilage open·2026
Same author

SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and therapeutic vulnerabilities.

Cancer discovery·2026
Same author

Genetic risk of chronic pain conditions associated with risk of suicide death through an integrative analysis of EHR and genomics data.

Translational psychiatry·2026
Same author

Quantitative reverse transcription PCR coupled with high-resolution melting for simultaneous detection and quantification of four isoforms of BCR::ABL1.

Journal of clinical pathology·2026
Same author

Genetic Liabilities to Neuropsychiatric Conditions in Suicide Deaths With No Prior Suicidality.

JAMA network open·2025
Same author

Different genetic liabilities to neuropsychiatric conditions in suicides with no prior suicidality.

medRxiv : the preprint server for health sciences·2025
Same journal

A Rapid Method for Accurately Determining Lipid Nanoparticle Size Using Nano-Flow Cytometry.

Journal of biomolecular techniques : JBT·2026
Same journal

Improving core facility service discovery with an AI assistant grounded in institutional web content.

Journal of biomolecular techniques : JBT·2026
Same journal

ABRF 2026 Awards.

Journal of biomolecular techniques : JBT·2026
Same journal

Multisite Assessment of Methods for Cell Preservation Upstream of Single-Cell RNA Sequencing.

Journal of biomolecular techniques : JBT·2026
Same journal

ABRF 2026 Meeting Report.

Journal of biomolecular techniques : JBT·2026
Same journal

Boosting Biomedical Research Capacity: The Role of INBRE-Supported Core Facility Vouchers in IDeA States.

Journal of biomolecular techniques : JBT·2026
See all related articles

This study introduces a novel DNA sequence alignment method using cross-correlation and the fast Fourier transform. This efficient algorithm accurately identifies sequence similarities, even with significant mutations or rearrangements.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • DNA sequence alignment is crucial for biological and medical advances.
  • Traditional methods include global and heuristic alignment algorithms.
  • Existing methods face challenges with efficiency and accuracy in complex scenarios.

Purpose of the Study:

  • To present a new sequence comparison approach using cross-correlation.
  • To demonstrate the computational efficiency via fast Fourier transform implementation.
  • To showcase the algorithm's versatility across various sequence alignment challenges.

Main Methods:

  • Utilized cross-correlation as the core mathematical operation for sequence comparison.
  • Implemented the algorithm with the fast Fourier transform for enhanced computational speed.

Related Experiment Videos

  • Applied the method to diverse biological sequence data, including DNA, RNA, and proteins.

    • Main Results:

    • Successfully aligned gene sequences in long genomic DNA stretches.
    • Identified sequence similarity in distantly related organisms.
    • Detected similarities despite up to 90% random point mutations and internal rearrangements (tandem repeats).
    • Investigated fusion proteins and demonstrated applicability to RNA and protein sequences.

    Conclusions:

    • The cross-correlation method offers an efficient, sensitive, and robust alternative for sequence alignment.
    • This approach excels in detecting similarities where traditional algorithms may falter.
    • The technique has broad applications in molecular biology and medicine.