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

RASCAL: rapid scanning and correction of multiple sequence alignments.

J D Thompson1, J C Thierry, O Poch

  • 1Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS/INSERM/ULP), B.P. 10142, 67404 Illkirch Cedex, France.

Bioinformatics (Oxford, England)
|June 13, 2003
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

Unusual <i>5f</i> magnetism in new kagome material UV<sub>6</sub>Sn<sub>6</sub>.

npj quantum materials·2025
Same author

The impact of technical and environmental conditions on the quality assessment in mammography.

Radiography (London, England : 1995)·2024
Same author

Normal Fermi Surface in the Nodal Superconductor CeCoIn_{5} Revealed via Thermal Conductivity.

Physical review letters·2024
Same author

Absence of Spontaneous Magnetic Fields due to Time-Reversal Symmetry Breaking in Bulk Superconducting UTe_{2}.

Physical review letters·2023
Same author

Constraints on the Decay of ^{180m}Ta.

Physical review letters·2023
Same author

A scoping review of clinical practices and adherence to UK national guidance related to the placement and position confirmation of adult nasogastric feeding tubes.

Radiography (London, England : 1995)·2022
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

This study introduces RASCAL, a novel knowledge-based method for refining multiple sequence alignments. RASCAL improves alignment accuracy and reliability by focusing corrections on less reliable regions, outperforming traditional iterative techniques.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) programs often introduce errors due to heuristic methods.
  • Iterative techniques are common for correcting alignment errors but can be inefficient.
  • A new knowledge-based approach offers an alternative refinement strategy.

Purpose of the Study:

  • To present RASCAL, a two-step refinement process for multiple sequence alignments.
  • To improve the reliability and efficiency of sequence alignment correction.
  • To offer an alternative to iterative error correction methods.

Main Methods:

  • A knowledge-based, two-step refinement strategy.
  • Dividing alignments into a 'lattice' to differentiate well-aligned regions.

Related Experiment Videos

  • Restricting alignment correction to less reliable regions.

    • Main Results:

    • RASCAL demonstrated significant improvements on BAliBASE alignments.
    • Alignment quality increased in 68% of 946 ProDom protein domain database alignments.
    • A high-quality alignment of 695 nuclear receptor proteins was generated in 11 minutes.

    Conclusions:

    • RASCAL provides a more reliable and efficient alignment refinement strategy.
    • The method successfully improves alignment quality without degrading existing high-quality regions.
    • RASCAL offers a valuable tool for bioinformatics research and large-scale sequence analysis.