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

Biological evaluation of d2, an algorithm for high-performance sequence comparison

W Hide1, J Burke, D B Davison

  • 1Department of Biochemical and Biophysical Sciences, University of Houston, TX 77204-5934, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|January 1, 1994
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

Fetal Alcohol Spectrum Disorder in Ireland.

Irish medical journal·2026
Same author

Correction: Measures of performance and proficiency in robotic assisted surgery: a systematic review.

Journal of robotic surgery·2025
Same author

Correction to: Measures of performance and proficiency in robotic assisted surgery: a systematic review.

Journal of robotic surgery·2024
Same author

Measures of performance and proficiency in robotic assisted surgery: a systematic review.

Journal of robotic surgery·2024
Same author

Animal factors that affect enteric methane production measured using the GreenFeed monitoring system in grazing dairy cows.

Journal of dairy science·2023
Same author

The Association of Surgeons in Training (ASiT) Consensus Statement on Major Trauma Training in the UK.

Annals of the Royal College of Surgeons of England·2023
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Asymmetric Drug-Drug Interaction Prediction Based on Generative Adversarial Networks and Knowledge Graph.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

The d2 algorithm offers a sensitive and selective method for rapid genetic sequence comparison. It efficiently detects novel biological relationships in large datasets, outperforming existing sequence alignment techniques.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Existing algorithms for sequence database searching rely on primary sequence similarity.
  • There is a need for efficient and sensitive methods to detect biologically significant similarities in large genetic datasets.

Purpose of the Study:

  • To determine the biological sensitivity and selectivity of the d2 comparison algorithm.
  • To evaluate d2's ability to detect biologically significant matches and novel sequence relationships.

Main Methods:

  • d2 algorithm utilizing sequence-word multiplicity for dissimilarity measurement.
  • Comparative analysis of d2's performance against existing methods on large genetic sequence datasets.
  • Optimization of d2 parameters (word-length, window size) using high-performance computing (Cray Y/MP-48).

Related Experiment Videos

Main Results:

  • d2 demonstrated high efficiency, comparing 884 bases against over 19 million bases in under a minute.
  • The algorithm successfully detected biologically significant matches and novel sequence relationships.
  • Analysis of dissimilarity score distributions within eukaryotic and prokaryotic GenBank divisions was performed.

Conclusions:

  • d2 is a unique, sensitive, and selective method for rapid sequence comparison.
  • The algorithm can identify sequence relationships missed by traditional alignment-based methodologies.
  • d2 offers a significant advancement in analyzing large-scale genetic data.