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

An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps

G J Barton1

  • 1Laboratory of Molecular Biophysics, University of Oxford, UK.

Computer Applications in the Biosciences : CABIOS
|December 1, 1993
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

Identifying joint-specific gait mechanisms causing impaired gait in alkaptonuria patients.

Gait & posture·2021
Same author

Leaving hip rotation out of a conventional 3D gait model improves discrimination of pathological gait in cerebral palsy: A novel neural network analysis.

Gait & posture·2019
Same author

Data on items of AKUSSI in Alkaptonuria collected over three years from the United Kingdom National Alkaptonuria Centre and the impact of nitisinone.

Data in brief·2018
Same author

Nitisinone arrests ochronosis and decreases rate of progression of Alkaptonuria: Evaluation of the effect of nitisinone in the United Kingdom National Alkaptonuria Centre.

Molecular genetics and metabolism·2018
Same author

Substrate and flow characteristics associated with White Sturgeon recruitment in the Columbia River Basin.

Heliyon·2018
Same author

A marker based kinematic method of identifying initial contact during gait suitable for use in real-time visual feedback applications.

Gait & posture·2012
Same journal

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Computer applications in the biosciences : CABIOS·1998
Same journal

Two applications to facilitate the viewing of database search result files on the Macintosh.

Computer applications in the biosciences : CABIOS·1998
Same journal

BioWish: a molecular biology command extension to Tcl/Tk.

Computer applications in the biosciences : CABIOS·1998
Same journal

The Sequence Alerting Server--a new WEB server.

Computer applications in the biosciences : CABIOS·1998
Same journal

A software tool for the analysis of mass spectrometric disulfide mapping experiments.

Computer applications in the biosciences : CABIOS·1998
Same journal

SAMBA: hardware accelerator for biological sequence comparison.

Computer applications in the biosciences : CABIOS·1998
See all related articles

This study introduces an efficient algorithm for finding multiple local sequence alignments, improving upon the Smith-Waterman method. It quickly identifies repeats and motifs in large sequence databases.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Sequence Analysis

Background:

  • Traditional sequence alignment algorithms like Smith-Waterman find only the single best local alignment.
  • Identifying multiple, non-intersecting local alignments is crucial for understanding complex biological sequences.
  • Existing methods can be computationally intensive for large datasets.

Purpose of the Study:

  • To develop an efficient algorithm for locating all non-intersecting locally optimal sequence alignments.
  • To enhance the identification of sequence repeats, multiple domains, and shuffled motifs.
  • To provide a fast method for scanning large sequence databanks on standard hardware.

Main Methods:

  • The algorithm builds upon the Smith-Waterman approach.

Related Experiment Videos

  • It utilizes a single pass through the comparison matrix to identify all optimal local alignments.
  • The method efficiently handles insertions and deletions within sequences.

    • Main Results:

    • The algorithm successfully identifies all non-intersecting locally optimal alignments in one pass.
    • It simplifies the detection of complex sequence features like repeats and shuffled motifs.
    • The method demonstrates sufficient speed for practical application on conventional workstations.

    Conclusions:

    • The described algorithm offers an efficient solution for finding multiple local sequence alignments.
    • It significantly improves the ability to analyze complex sequence structures and large datasets.
    • This approach is valuable for large-scale sequence database scanning in bioinformatics.