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

Detecting distant homology with Meta-BASIC.

Krzysztof Ginalski1, Marcin von Grotthuss, Nick V Grishin

  • 1Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA. kginal@bioinfo.pl

Nucleic Acids Research
|June 25, 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

TAK-994 mechanistic investigation into drug-induced liver injury.

Toxicological sciences : an official journal of the Society of Toxicology·2025
Same author

A phase 1/2 safety and efficacy study of TAK-754 gene therapy: The challenge of achieving durable factor VIII expression in haemophilia A clinical trials.

Haemophilia : the official journal of the World Federation of Hemophilia·2024
Same author

Rare A360T Mutation Alters GSK3β(Ser9) Binding in the Cytosolic Loop of Presenilin 1, Influencing β-Catenin Nuclear Localization and Pro-Death Gene Expression in Alzheimer's Disease Case.

International journal of molecular sciences·2023
Same author

The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits.

Cell metabolism·2023
Same author

High-throughput genetic clustering of type 2 diabetes loci reveals heterogeneous mechanistic pathways of metabolic disease.

Diabetologia·2022
Same author

Who Is at Risk of Developing Cannabis Dependence? Findings From an Extensive Online Study on Cannabis Users.

Journal of addictions nursing·2022
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Meta-BASIC identifies distant protein similarities using consensus alignments of meta profiles. This sensitive, high-throughput method aids in assigning functions to unknown protein families, outperforming many existing servers.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Protein sequence similarity detection is crucial for functional annotation.
  • Existing methods struggle with identifying very distant evolutionary relationships.
  • High-throughput functional assignment for uncharacterized proteins remains a challenge.

Purpose of the Study:

  • To introduce Meta-BASIC, a novel computational approach for sensitive detection of distant protein similarity.
  • To evaluate Meta-BASIC's performance against existing protein recognition servers.
  • To apply Meta-BASIC for functional annotation of protein families with unknown function (DUF).

Main Methods:

  • Meta-BASIC utilizes consensus alignments of meta profiles combined with predicted secondary structures.

Related Experiment Videos

  • It employs multiple scoring systems and alignment algorithms for robust comparison.
  • Benchmarking involved comparison with individual and meta-prediction servers.

    • Main Results:

    • Meta-BASIC demonstrates superior performance compared to many individual servers and competes with structure-based meta predictors.
    • The method successfully detects very distant protein relationships, even without known tertiary structures.
    • Application to 860 PfamA DUFs yielded numerous novel structure-functional assignments.

    Conclusions:

    • Meta-BASIC is a sensitive, high-throughput tool for recognizing distant protein similarities.
    • It offers a valuable approach for annotating uncharacterized proteins, particularly those in PfamA.
    • Novel functional assignments for DUF271 (nucleotide-diphospho-sugar transferase) and DUF431 (RNA methyltransferase) were proposed.