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The SYSTERS protein sequence cluster set.

A Krause1, J Stoye, M Vingron

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

Nucleic Acids Research
|December 11, 1999
PubMed
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The SYSTERS protein database classifies protein sequences into families, superfamilies, and subfamilies. This resource aids researchers in protein analysis and discovery using various search tools and domain information.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein sequence databases like SWISS-PROT and PIR are crucial for biological research.
  • Classifying protein sequences into families facilitates understanding of protein function and evolution.
  • Existing classification methods may lack comprehensive hierarchical structures or integrated domain information.

Purpose of the Study:

  • To introduce the SYSTERS (SYSTEmatic Re-Searching) protein sequence cluster set.
  • To provide a hierarchical classification of protein sequences from major databases.
  • To offer integrated tools for searching, aligning, and annotating protein families.

Main Methods:

  • Clustering of all SWISS-PROT and PIR protein sequences into disjoint families, superfamilies, and subfamilies.

Related Experiment Videos

  • Development and integration of the SSMAL search tool alongside traditional BLAST and FASTA for sequence searching.
  • Generation of multiple sequence alignments for each cluster, annotated with Pfam domain information.
  • Incorporation of NCBI taxonomy for a taxonomic overview of organisms within each cluster.

    • Main Results:

    • Creation of a comprehensive, hierarchically structured protein sequence cluster set (SYSTERS).
    • Successful integration of multiple search tools (SSMAL, BLAST, FASTA) for querying the cluster set.
    • Annotation of clusters with domain information from the Pfam database.
    • Provision of a taxonomic overview for each protein cluster.
    • Availability of the SYSTERS cluster set for public querying and browsing online.

    Conclusions:

    • The SYSTERS protein cluster set offers a valuable, integrated resource for protein sequence analysis.
    • The hierarchical classification and integrated annotation facilitate deeper insights into protein families and their evolution.
    • SYSTERS enhances protein research by providing efficient search, alignment, and domain analysis capabilities.