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Related Experiment Videos

Proclass protein family database: new version with motif alignments

C H Wu1, S Shivakumar

  • 1Department of Epidemiology/Biomathematics, University of Texas Health Center at Tyler 75710, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|August 11, 1998
PubMed
Summary

The ProClass protein family database organizes sequence entries into families using ProSite patterns and PIR superfamilies. This enhanced version increases motif collection by 50% and links to multiple databases for improved genomic annotation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein sequence databases require effective organization for biological research.
  • Classifying protein sequences into families aids in understanding function and evolution.
  • Existing databases like ProSite and PIR-International provide valuable protein family information.

Purpose of the Study:

  • To present an updated version of the ProClass protein family database.
  • To enhance protein sequence organization and information retrieval.
  • To support comprehensive genomic annotation through improved family classification.

Main Methods:

  • Organizing non-redundant sequence entries into families using ProSite patterns and PIR superfamilies.
  • Integrating data from SwissProt and PIR-International databases.

Related Experiment Videos

  • Utilizing the GeneFIND family identification system to detect new members.
  • Incorporating gapped motif alignments for ProSite patterns.

    • Main Results:

    • The ProClass database now contains approximately 100,000 entries, with over half classified into about 3,000 families.
    • The new version includes links to diverse protein family, domain, and structural class databases.
    • The motif collection has increased by 50% compared to previous versions.
    • Numerous new protein family members were identified using the GeneFIND system.

    Conclusions:

    • The ProClass database effectively organizes protein sequences, maximizing family information retrieval.
    • The database serves as a valuable tool for organizing protein sequence data and aiding genomic annotation.
    • The expanded motif collection and cross-database links enhance its utility for researchers.