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

Automata-theoretic models of mutation and alignment

D B Searls1, K P Murphy

  • 1Department of Genetics University of Pennsylvania School of Medicine, Philadelphia 19104-6145, USA.

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1995
PubMed
Summary

Finite-state transducers model biological mutation mechanisms. This study adapts weighted transducers into string edit machines, enabling rapid design of novel alignment algorithms through a visual programming system.

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

Assessment of isocenter alignment during CT colonography: Implications for clinical practice.

Radiography (London, England : 1995)·2018
Same author

Radiation exposure from diagnostic imaging in young patients with testicular cancer.

European radiology·2014
Same author

Non-contrast CT at comparable dose to an abdominal radiograph in patients with acute renal colic; impact of iterative reconstruction on image quality and diagnostic performance.

Insights into imaging·2014
Same author

CT fluoroscopically guided percutaneous placement of transiliosacral rod for sacral insufficiency fracture: case report and technique.

AJNR. American journal of neuroradiology·2007
Same author

Tibioperoneal angioplasty and bypass.

Acta chirurgica Belgica·2003
Same author

Mining the bibliome.

The pharmacogenomics journal·2002

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Algorithm Design

Background:

  • Finite-state transducers are computational models with input and output capabilities.
  • These models can represent simple biological mutation processes.
  • Existing alignment algorithms often rely on dynamic programming and recurrence relations.

Purpose of the Study:

  • To develop a methodology for adapting finite-state transducers into string edit machines.
  • To create a system for rapid prototyping of new sequence alignment algorithms.
  • To bridge the gap between mutation modeling and algorithmic design in bioinformatics.

Main Methods:

  • Utilizing numerically-weighted finite-state transducers.
  • Mechanically adapting transducer specifications into string edit machines.

Related Experiment Videos

  • Developing a visual programming system for algorithm design.

    • Main Results:

    • String edit machines equivalent to dynamic programming recurrence relations were created.
    • A functional visual programming system for rapid algorithm prototyping was developed.
    • The methodology facilitates the design of novel alignment algorithms.

    Conclusions:

    • Finite-state transducers provide a viable framework for developing sequence alignment algorithms.
    • The visual programming system accelerates the design and testing of bioinformatics tools.
    • This approach offers a novel perspective on modeling biological mutations and sequence analysis.