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

Multiple protein sequence alignment using double-dynamic programming.

W R Taylor1, G Saelensminde, I Eidhammer

  • 1Division of Mathematical Biology, National Institute for Medical Research, London, UK. w_taylor@nimr.mrc.ac.uk

Computers & Chemistry
|January 22, 2000
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

Can tibio-femoral kinematic and kinetic parameters reveal poor functionality and underlying deficits after total knee replacement? A systematic review.

The Knee·2021
Same author

In Vivo Elongation Patterns of the Collateral Ligaments in Healthy Knees During Functional Activities.

The Journal of bone and joint surgery. American volume·2021
Same author

Length-Change Patterns of the Collateral Ligaments During Functional Activities After Total Knee Arthroplasty.

Annals of biomedical engineering·2020
Same author

Author Correction: Tibio-Femoral Contact Force Distribution is Not the Only Factor Governing Pivot Location after Total Knee Arthroplasty.

Scientific reports·2019
Same author

Tibio-Femoral Contact Force Distribution is Not the Only Factor Governing Pivot Location after Total Knee Arthroplasty.

Scientific reports·2019
Same author

Analysis of the role of GSK3 in the mitotic checkpoint.

Scientific reports·2018
Same journal

Constructing a useful tool for characterizing amino acid conformers by means of quantum chemical and graph theory indices.

Computers & chemistry·2002
Same journal

CLiBE: a database of computed ligand binding energy for ligand-receptor complexes.

Computers & chemistry·2002
Same journal

On the solution of mixed-integer nonlinear programming models for computer aided molecular design.

Computers & chemistry·2002
Same journal

Use of the Numerov method to improve the accuracy of the spatial discretisation in finite-difference electrochemical kinetic simulations.

Computers & chemistry·2002
Same journal

Automatic identification by 13C NMR of substituent groups bonded in natural product skeletons.

Computers & chemistry·2002
Same journal

A new redundant variable pruning approach--minor latent variable perturbation-PLS used for QSAR studies on anti-HIV drugs.

Computers & chemistry·2002
See all related articles

This study introduces a novel multiple sequence alignment method using double dynamic programming (DDP). The DDP approach effectively reconciles pairwise alignment inconsistencies, yielding results comparable to standard progressive methods in a single pass.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding protein evolution and function.
  • Existing MSA methods face challenges in reconciling pairwise alignment inconsistencies.
  • Previous applications of double dynamic programming (DDP) focused on structural constraints.

Purpose of the Study:

  • To develop a novel MSA method based on the DDP algorithm.
  • To address and reconcile inconsistencies in combining pairwise alignments into a multiple alignment.
  • To evaluate the efficiency and accuracy of the new DDP-based MSA method.

Main Methods:

  • The method employs double dynamic programming (DDP) to reconcile pairwise alignment inconsistencies.

Related Experiment Videos

  • Low-level alignments (paths) are summed into a matrix for a high-level alignment.
  • Pairwise alignment results are combined in a multiple sequence alignment program.
  • Iterative refinement using selected constraints was explored but found unnecessary.

    • Main Results:

    • The DDP-based method effectively reconciles inconsistencies from pairwise alignments.
    • A single-pass application of the method produced results comparable to standard progressive alignment.
    • The iterative refinement step did not improve alignment quality.

    Conclusions:

    • The novel DDP-based method offers an efficient and accurate approach to multiple sequence alignment.
    • The method successfully overcomes limitations of combining pairwise alignments.
    • Future applications in structural bioinformatics and related fields are promising.