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

Construction of validated, non-redundant composite protein sequence databases.

A J Bleasby1, J C Wootton

  • 1Departments of Genetics and Biophysics, University of Leeds, UK.

Protein Engineering
|January 1, 1990
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

Expression of the Escherichia coli glutamate dehydrogenase gene in the cyanobacterium Synechococcus PCC6301 causes ammonium tolerance.

Plant molecular biology·2013
Same author

Rural medicine: implications for the future.

Canadian family physician Medecin de famille canadien·2011
Same author

[Not Available].

Canadian family physician Medecin de famille canadien·2011
Same author

A secreted serine-threonine kinase determines virulence in the eukaryotic pathogen Toxoplasma gondii.

Science (New York, N.Y.)·2006
Same author

Spirit of inquiry.

Journal of alternative and complementary medicine (New York, N.Y.)·2002
Same author

Surveys of complementary and alternative medicine: part IV. Use of alternative and complementary therapies for rheumatologic and other diseases.

Journal of alternative and complementary medicine (New York, N.Y.)·2002

A new strategy creates a comprehensive protein sequence database by automating data amalgamation and redundancy elimination. This modular approach ensures validated entries for improved sequence similarity searching and information retrieval.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein sequence databases are crucial for biological research.
  • Existing databases often contain redundant or trivially different entries.
  • A need exists for a validated, comprehensive, and easily updatable composite database.

Purpose of the Study:

  • To develop a strategy for constructing a validated, comprehensive composite protein sequence database.
  • To implement a modular and automated process for data amalgamation and redundancy elimination.
  • To facilitate efficient sequence similarity searching and information retrieval.

Main Methods:

  • Amalgamation of entries from multiple primary source databases.
  • Automated processes for eliminating redundant and trivially different entries.

Related Experiment Videos

  • A modular approach allowing scientific judgment at each stage.
  • Prioritization of source databases based on sequence validation quality.
  • Pairwise comparison and rejection of entries based on defined redundancy criteria.
  • Implementation of efficient algorithms within the COMPO software system.

    • Main Results:

    • Successful construction and regular updating of the OWL composite protein sequence database.
    • Demonstration of the COMPO system's efficiency in processing and integrating data from diverse sources (NBRF-PIR, SWISS-PROT, GenBank, etc.).
    • Revelation of the extent of redundancy within primary protein sequence databases through the comparison process.

    Conclusions:

    • The developed strategy and COMPO software provide a robust method for creating and maintaining a high-quality composite protein sequence database.
    • The modular approach facilitates frequent updates, ensuring data relevance.
    • A comprehensive composite database significantly enhances sequence similarity searching and information retrieval capabilities.