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Database of protein sequence alignments: PIR-ALN

G Y Srinivasarao1, L S Yeh, C R Marzec

  • 1Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road N.W., Washington, DC 20007, USA. geetha@nbrf.georgetown.edu

Nucleic Acids Research
|December 10, 1998
PubMed
Summary

The Protein Information Resource (PIR) provides curated protein sequence alignments, aiding in sequence classification and standardization. This database facilitates research by offering accessible, updated alignment data for protein families and superfamilies.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Information Resource (PIR) has been a key resource for protein sequence data since 1991.
  • Curated protein sequence alignments are crucial for understanding protein function and evolution.
  • Standardization of protein nomenclature and features is essential for data sharing and interpretation.

Purpose of the Study:

  • To describe the Protein Information Resource (PIR) database of curated protein sequence alignments.
  • To highlight the utility of the PIR database in protein classification and standardization.
  • To provide information on accessing and querying the PIR alignment data.

Main Methods:

  • Generation of multiple sequence alignments using CLUSTAL V/W.

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  • Interactive checking and correction of alignments using ALNED.
  • Utilizing the ATLAS information retrieval system for browsing and querying.

    • Main Results:

    • The PIR database contains superfamily, family, and homology domain alignments.
    • The database has facilitated sequence classification and the definition of new homology domains.
    • Standardized protein names, features, and keywords have been disseminated.

    Conclusions:

    • The PIR database serves as a valuable resource for protein sequence analysis and research.
    • The integration of alignment generation, editing, and retrieval tools enhances data usability.
    • Regular updates ensure the database remains current and relevant for the scientific community.