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

Parallelization of a local similarity algorithm.

X Huang1, W Miller, S Schwartz

  • 1Department of Computer Science, Michigan Technological University, Houghton 49931.

Computer Applications in the Biosciences : CABIOS
|April 1, 1992
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

Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure.

Molecular biology and evolution·2007
Same author

Global predictions and tests of erythroid regulatory regions.

Cold Spring Harbor symposia on quantitative biology·2004
Same author

Association between divergence and interspersed repeats in mammalian noncoding genomic DNA.

Proceedings of the National Academy of Sciences of the United States of America·2001
Same author

Databases of human hemoglobin variants and other resources at the globin gene server.

Hemoglobin·2001
Same author

Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement.

Molecular and cellular biology·2001
Same author

New views of evolution and regulation of vertebrate beta-like globin gene clusters from an orphaned gene in marsupials.

Proceedings of the National Academy of Sciences of the United States of America·2001
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

A new parallel algorithm efficiently finds similar regions in two sequences using less memory. This method offers rapid, high-resolution alignments for biological sequence comparison.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The local similarity problem involves identifying shared segments within two biological sequences.
  • Traditional algorithms for local similarity require substantial computational space, proportional to the product of sequence lengths.
  • Recent advancements introduced a dynamic programming algorithm with reduced space complexity, proportional to the sum of sequence lengths.

Purpose of the Study:

  • To parallelize the recently developed space-efficient dynamic programming algorithm for local similarity.
  • To evaluate the performance of the parallelized algorithm through experimental studies.
  • To enhance the capabilities of software toolkits for pairwise sequence comparison.

Main Methods:

  • Parallelization of a novel dynamic programming algorithm for local sequence alignment.

Related Experiment Videos

  • Implementation and testing on an Intel hypercube parallel computing platform.
  • Application to comparative genomics, specifically analyzing chloroplast genomes.

    • Main Results:

    • The parallel algorithm successfully reduces memory requirements for local similarity searches.
    • Experimental results demonstrate rapid and high-resolution sequence alignments.
    • The method proved effective in comparing complex genomic data, such as chloroplast genomes.

    Conclusions:

    • The parallelized algorithm offers a significant improvement in computational efficiency for local similarity problems.
    • This approach provides a valuable tool for rapid and accurate pairwise sequence comparison in bioinformatics.
    • The findings facilitate high-resolution genomic analysis and comparative studies.