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Related Experiment Videos

Pfam: clans, web tools and services.

Robert D Finn1, Jaina Mistry, Benjamin Schuster-Böckler

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. rdf@sanger.ac.uk

Nucleic Acids Research
|December 31, 2005
PubMed
Summary
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Pfam, a protein family database, now includes clans for grouping related families. New web pages, tools, and web services enhance programmatic access to this vital bioinformatics resource.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pfam is a widely used database cataloging protein families.
  • Protein family classification is crucial for understanding protein function and evolution.
  • Previous versions lacked a hierarchical structure for related families.

Purpose of the Study:

  • To introduce Pfam clans, a new hierarchical grouping of related protein families.
  • To describe enhancements to Pfam web tools and introduce web services for programmatic access.
  • To detail the structure and accessibility of the updated Pfam database.

Main Methods:

  • Development of a clan-based organizational structure within the Pfam database.
  • Implementation of new web pages and user interfaces for clan information.

Related Experiment Videos

  • Creation of web services (APIs) for automated data retrieval and analysis.

    • Main Results:

    • Pfam release 18.0 contains 7973 protein family entries, now organized into clans.
    • New web pages provide detailed descriptions and access to Pfam clan data.
    • Introduction of web services enables efficient programmatic interaction with Pfam data and tools.

    Conclusions:

    • Pfam clans offer a more organized view of protein sequence and domain relationships.
    • Enhanced web tools and services improve the utility and accessibility of Pfam.
    • The updated Pfam database serves as a more powerful resource for biological research.