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

PARODS--a study of parallel algorithms for ordering DNA sequences

S M Bhandarkar1, S Chirravuri, J Arnold

  • 1Department of Computer Science, University of Georgia, Athens 30602-7404, USA. suchi@cs.uga.edu

Computer Applications in the Biosciences : CABIOS
|August 1, 1996
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

Osteoarthritis consumers as co-researchers: identifying consumer insights to improve osteoarthritis management by co-designing translational research solutions.

Osteoarthritis and cartilage·2023
Same author

Design and function of targeted endocannabinoid nanoparticles.

Scientific reports·2022
Same author

Epilepsy and the smell of fear.

Epilepsy & behavior : E&B·2021
Same author

Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa.

Scientific reports·2020
Same author

Boot camps in neonatal-perinatal medicine fellowship programs: A national survey.

Journal of neonatal-perinatal medicine·2019
Same author

Fragile: Please handle with care.

Radiography (London, England : 1995)·2018

This study introduces PARODS, parallel algorithms for DNA sequence ordering using simulated annealing. The best algorithm achieved a speedup of 1000x on a 2048-processor system for physical mapping.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Algorithm Development

Background:

  • Physical mapping of DNA sequences is crucial for genome assembly.
  • Existing serial algorithms for DNA mapping can be computationally intensive.
  • Parallel computing offers potential for accelerating complex biological sequence analysis.

Purpose of the Study:

  • To develop and evaluate a suite of parallel algorithms for DNA sequence ordering.
  • To adapt simulated annealing for efficient physical mapping on parallel architectures.
  • To analyze the performance, speedup, and scalability of parallel mapping algorithms.

Main Methods:

  • Development of parallel algorithms for simulated annealing based on Markov chain decomposition.
  • Application of perturbation methods and annealing heuristics tailored for DNA mapping.

Related Experiment Videos

  • Implementation of Single Instruction Multiple Data (SIMD) on MasPar MP-2 and Multiple Instruction Multiple Data (MIMD) on Intel iPSC/860 systems.

    • Main Results:

    • The PARODS suite includes parallel algorithms for DNA sequence ordering and physical mapping.
    • SIMD implementations on a 2048-processor MasPar MP-2 achieved a speedup of approximately 1000.
    • MIMD implementations on an 8-processor Intel iPSC/860 achieved a speedup of approximately 5.

    Conclusions:

    • Parallel simulated annealing algorithms can significantly accelerate DNA physical mapping.
    • SIMD architectures demonstrate superior scalability and speedup for this class of algorithms compared to MIMD.
    • The PARODS algorithms provide an efficient computational framework for large-scale DNA sequence ordering.