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

MoDEL: an efficient strategy for ungapped local multiple alignment.

David Hernandez1, Robin Gras, Ron Appel

  • 1Proteome Informatics Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH 1211 Geneva 4, Switzerland. david.hernandez@isb-sib.ch

Computational Biology and Chemistry
|May 8, 2004
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

Stent retriever-assisted intra-arterial lysis for distal vessel occlusions: a feasible pharmacomechanical rescue strategy.

Journal of neurointerventional surgery·2026
Same author

CpG-ODN/Coa-ASC16 nanostructured adjuvant platform as a safe and effective alternative in Bothrops diporus antivenom production.

Archives of toxicology·2026
Same author

Meckel's Diverticulum as a Rare Etiology of Small-Bowel Obstruction in an Otherwise Healthy Adult: A Case Report.

Cureus·2026
Same author

Endovascular Treatment for Medium and Distal Vessel Occlusion Stroke: Are We Missing the Point?

Stroke (Hoboken, N.J.)·2026
Same author

Refining thrombectomy benefit in medium vessel occlusion (MeVO) strokes using imaging and clinical enrichment.

Journal of neurointerventional surgery·2026
Same author

Balloon-Expandable Stenting as a Bridging Therapy in Patients With Acute Stroke and Tandem Occlusions.

Stroke (Hoboken, N.J.)·2026
Same journal

An interpretable framework for cancer drug response prediction using integrated drug and multi-omics data with a hybrid Bi-LSTM-GRU network.

Computational biology and chemistry·2026
Same journal

SegMWB: A lightweight deep learning framework for microscopic image classification.

Computational biology and chemistry·2026
Same journal

Protein dynamic simulations: From early inception to clinical translation over half a century.

Computational biology and chemistry·2026
Same journal

Integrated omics and virtual screening predict Tabularin as a dual inhibitor of the prognostic microRNAs mir-19a and mir-32 in colorectal cancer.

Computational biology and chemistry·2026
Same journal

In silico characterization of acetyl-CoA carboxylase from Staphylococcus aureus and Escherichia coli: A comparative analysis.

Computational biology and chemistry·2026
Same journal

An optimized cascaded transformer with progressive attention for lung and colon cancer diagnosis from histopathological images.

Computational biology and chemistry·2026
See all related articles

We present a novel ungapped local multiple alignment (ULMA) method using linked evolutionary and hill-climbing searches. This approach effectively refines sequence alignments for biological data analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment is crucial for understanding protein and nucleotide sequence relationships.
  • Existing methods may face challenges with difficult or artificial datasets.

Purpose of the Study:

  • To introduce a new method for ungapped local multiple alignment (ULMA).
  • To improve the accuracy and efficiency of sequence alignment for biological data.

Main Methods:

  • A linked optimization strategy exploring two search spaces: global evolutionary search and local hill-climbing.
  • Utilizing relative entropy as an objective function for refinement.
  • Coupling search spaces by projecting high-scoring results.

Main Results:

Related Experiment Videos

  • Demonstrated advantages of the ULMA strategy on challenging natural amino acid sequences.
  • Validated the method's effectiveness using artificial datasets.
  • Achieved refined sequence alignments through local search optimization.

Conclusions:

  • The proposed ULMA method offers a robust approach to sequence alignment.
  • The linked optimization strategy enhances alignment quality.
  • A web interface is available for broader accessibility.