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

New flexible approaches for multiple sequence alignment

T Shibuya1, H Imai

  • 1Department of Information Science, Faculty of Science, University of Tokyo, Japan.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 1, 1997
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

Decreased physical performance of congenic mice with mismatch between the nuclear and the mitochondrial genome.

Genes & genetic systems·1998
Same author

Identification of a new intermediate state that binds but not activates transducin in the bleaching process of bovine rhodopsin.

FEBS letters·1998
Same author

Contribution of foregut endoderm to tooth initiation of mandibular incisor in rat embryos.

European journal of oral sciences·1998
Same author

Interleukin-1 receptor antagonist inhibits transient increase of plasma corticosterone in the initial phase of trimethyltin-induced hippocampal necrosis.

Neurotoxicology·1998
Same author

Glomerulopathy due to chronic infection of Propionibacterium acnes in a patient with Felty's syndrome.

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association·1998
Same author

Crescentic glomerulonephritis accompanied by myeloperoxidase-antineutrophil cytoplasmic antibodies in a patient having myelodysplastic syndrome with trisomy 7.

American journal of kidney diseases : the official journal of the National Kidney Foundation·1998
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Asymmetric Drug-Drug Interaction Prediction Based on Generative Adversarial Networks and Knowledge Graph.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

This study introduces two novel methods for multiple sequence alignment, offering numerous suboptimal alignments and enabling parametric analysis. These approaches enhance biological significance beyond just optimal alignments for protein structure and phylogeny.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Multiple sequence alignment (MSA) is crucial for protein structure prediction and phylogenetic inference.
  • Optimal alignments may not always reflect biological significance due to fixed scoring criteria.
  • Investigating suboptimal and parametrically varied alignments is essential for deeper biological insights.

Purpose of the Study:

  • To develop flexible and efficient methods for addressing limitations in traditional MSA.
  • To enable the exploration of suboptimal alignments and the impact of parameter variations in MSA.
  • To improve the biological relevance of MSA findings in molecular biology.

Main Methods:

  • Enumeration of suboptimal alignments using Eppstein algorithm and an efficient algorithm for necessary alignments.

Related Experiment Videos

  • Parametric analysis techniques for multiple sequence alignment problems.
  • Experimental validation using diverse protein sequence datasets.

    • Main Results:

    • Demonstrated feasibility of enumerating necessary suboptimal alignments for MSA.
    • Developed and tested methods for parametric multiple sequence alignment.
    • Evaluated the efficiency and properties of the proposed algorithms on real protein sequences.

    Conclusions:

    • The proposed methods offer significant improvements for exploring biological significance in MSA.
    • Suboptimal and parametric analyses provide valuable alternatives to solely optimal alignments.
    • These advancements enhance the utility of MSA in fields like structural biology and phylogenetics.