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Related Experiment Videos

Sequence harmony: detecting functional specificity from alignments.

K Anton Feenstra1, Walter Pirovano, Klaas Krab

  • 1Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

Nucleic Acids Research
|June 23, 2007
PubMed
Summary
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Sequence Harmony (SH) web server identifies key protein residues. It scores compositional differences to find subtype-specific sites, aiding in protein structure and function analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Multiple sequence alignments are crucial for identifying specificity-determining residues in protein families.
  • Existing methods often rely on conservation, which may overlook important subfamily-specific variations.

Purpose of the Study:

  • To present a web server implementation of the Sequence Harmony (SH) method.
  • To enable accurate detection of subfamily-specific positions in protein alignments.
  • To facilitate the mapping of predicted sites onto protein structures.

Main Methods:

  • The Sequence Harmony (SH) method scores compositional differences between subfamilies within a multiple sequence alignment.
  • A web server was developed for user-friendly access to the SH method.

Related Experiment Videos

  • Predicted sites can be visualized on protein structures.

    • Main Results:

    • The SH web server accurately detects subfamily-specific positions without requiring conservation.
    • Application to plant mitochondrial alternative oxidases (AOX) demonstrated its utility.
    • Predicted sites were found to cluster in specific regions on an AOX homology model, integrating sequence and structural data.

    Conclusions:

    • The SH web server provides an efficient tool for identifying functionally important residues.
    • Combining sequence and structural information enhances the understanding of protein function and evolution.
    • The SH server is accessible at www.ibi.vu.nl/programs/seqharmwww.