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

Local weighting schemes for protein multiple sequence alignment.

Jaap Heringa1

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

Computers & Chemistry
|July 30, 2002
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

Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers.

NPJ precision oncology·2025
Same author

High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue.

The Journal of molecular diagnostics : JMD·2024
Same author

CIBRA identifies genomic alterations with a system-wide impact on tumor biology.

Bioinformatics (Oxford, England)·2024
Same author

Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.

Bioinformatics (Oxford, England)·2023
Same author

Author Correction: Applying federated learning to combat food fraud in food supply chains.

NPJ science of food·2023
Same author

Applying federated learning to combat food fraud in food supply chains.

NPJ science of food·2023
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

New weighting schemes enhance progressive multiple sequence alignment accuracy. Local profile pre-processing improved alignment quality by 5.5%, with iteration adding further gains.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate multiple sequence alignment (MSA) is crucial for understanding protein and nucleic acid evolution and function.
  • Existing progressive MSA methods can be limited by information propagation and scoring functions.

Purpose of the Study:

  • To introduce and evaluate novel weighting schemes for progressive MSA.
  • To enhance the accuracy and reliability of MSA through improved pre-processing and alignment strategies.

Main Methods:

  • Developed three weighting schemes: global profile pre-processing, local profile pre-processing, and local-global alignment using double dynamic programming (DDP).
  • Implemented these schemes within the PRALINE MSA software, incorporating iterative refinement modes.
  • Evaluated performance using the BAliBASE benchmark alignment database.

Related Experiment Videos

Main Results:

  • Local profile pre-processing significantly improved alignment quality by 5.5% compared to default PRALINE settings.
  • Iterative refinement further enhanced alignment quality by an additional percentage point.
  • The PRALINE toolbox demonstrated high-quality alignment generation capabilities.

Conclusions:

  • The proposed weighting schemes, particularly local profile pre-processing, offer substantial improvements in MSA accuracy.
  • Iterative approaches combined with refined weighting schemes are effective for enhancing alignment quality.
  • The study highlights the importance of scoring functions and benchmarking in evaluating MSA methods.