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

A set-theoretic approach to database searching and clustering

A Krause1, M Vingron

  • 1Deutsches Krebsforschungszentrum (DKFZ), Theoretische Bioinformatik, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. a.krause@dkfz-heidelberg.de

Bioinformatics (Oxford, England)
|July 31, 1998
PubMed
Summary

We developed an iterative database searching method for protein sequence clustering. This approach automatically assigns 80% of SWISS-PROT sequences into distinct clusters efficiently.

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

HIV-Gag VLP-based vaccine purification at manufacturing scale: Combination of counterflow centrifugation and nuclease treatment as a key to DNA depletion.

New biotechnology·2026
Same author

Erratum to "Augmenting approaches to AMR prevention: a case for environmental sustainability within the WHO core components for infection prevention and control" [J Hosp Infect 165 (2025) 118-127].

The Journal of hospital infection·2025
Same author

Case Report: <i>FBN1</i> mutation screening in South African patients with Marfan syndrome.

Frontiers in genetics·2025
Same author

Breast cancer germline multigene panel testing in mainstream oncology based on clinical-public health utility: ESMO Precision Oncology Working Group recommendations.

Annals of oncology : official journal of the European Society for Medical Oncology·2025
Same author

Optimizing nuclease treatment to enhance anion exchange chromatography of HIV-derived virus-like particles.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences·2025
Same author

[Rheumatological care in Germany : Memorandum of the German Society for Rheumatology and Clinical Immunology 2024].

Zeitschrift fur Rheumatologie·2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein sequence databases are essential for biological research.
  • Efficiently clustering these large datasets is crucial for analysis.
  • Existing methods may be time-consuming or lack automation.

Purpose of the Study:

  • To introduce an iterative database searching method.
  • To develop an automated protein database clustering algorithm.
  • To improve the efficiency and accuracy of sequence clustering.

Main Methods:

  • Iterative database searching algorithm.
  • Set-theoretic analysis for cluster refinement.
  • Application to PIR1 and SWISS-PROT databases.

Related Experiment Videos

Main Results:

  • Unambiguous assignment of 80% of SWISS-PROT sequences to clusters.
  • Fully automated clustering process.
  • Fast clustering without all-against-all comparisons.

Conclusions:

  • The developed method enables rapid and accurate clustering of large protein sequence datasets.
  • The automated approach facilitates efficient database management and analysis.
  • The clustering results are validated against expert-generated data.