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Related Experiment Videos

Blocks-based methods for detecting protein homology.

J G Henikoff1, S Pietrokovski, C M McCallum

  • 1Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. steveh@fhcrc.org

Electrophoresis
|June 28, 2000
PubMed
Summary
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The Blocks+ database offers tools for searching protein and DNA sequences to identify distant relationships. This resource aids in protein family analysis and includes features like sequence logos and PCR primer design.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Conserved protein regions are key indicators of protein family relationships.
  • Multiple aligned sequence segments, termed blocks, represent these conserved regions.
  • Existing databases like PROSITE, Prints, Pfam-A, ProDom, and Domo contain valuable protein family information.

Purpose of the Study:

  • To introduce the Blocks+ Database and its associated World Wide Web and e-mail servers.
  • To describe new features for detecting distant protein relationships using sequence blocks.
  • To provide tools for comprehensive protein family analysis and related applications.

Main Methods:

  • Utilizing multiple sequence alignments to define conserved blocks.
  • Developing search tools for DNA and protein queries against the Blocks+ Database.

Related Experiment Videos

  • Integrating data from multiple protein family databases (PROSITE, Prints, Pfam-A, ProDom, Domo).
  • Implementing search algorithms like BLIMPS and IMPALA for enhanced searching capabilities.

    • Main Results:

    • The Blocks+ Database provides a unified resource for protein family information.
    • New features enable the detection of distant evolutionary relationships between proteins.
    • Tools for visualization (sequence logos, phylogenetic trees, 3D structure display) are available.
    • A strategy for designing polymerase chain reaction (PCR) primers based on blocks is presented.

    Conclusions:

    • The Blocks+ Database is a valuable resource for exploring protein sequence conservation and relationships.
    • The integrated approach enhances the ability to discover evolutionary links between protein families.
    • The provided tools support various downstream applications in molecular biology and bioinformatics research.