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Related Experiment Videos

Alignment of protein sequences using secondary structure: a modified dynamic programming method.

F Fischel-Ghodsian1, G Mathiowitz, T F Smith

  • 1Molecular Biology Computer Research Resource, Dana-Farber Cancer Institute, Boston, MA 02115.

Protein Engineering
|July 1, 1990
PubMed
Summary
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This study introduces STRALIGN, a novel method for comparing protein sequences using both primary and secondary structures. STRALIGN significantly improves sequence alignment accuracy, especially for proteins with low primary sequence similarity.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein sequence comparison is crucial for understanding protein function and evolution.
  • Existing methods primarily rely on primary sequence information, which can be limiting for distantly related proteins.

Purpose of the Study:

  • To develop and evaluate a novel method for protein sequence comparison that incorporates both primary and secondary structure information.
  • To assess the effectiveness of the new method in improving sequence alignment accuracy, particularly for proteins with low primary sequence similarity.

Main Methods:

  • Protein sequences were annotated with predicted secondary structures using a modified Chou-Fasman method.
  • Two-lettered code sequences (amino acid and secondary structure) were generated.

Related Experiment Videos

  • A dynamic programming method (STRALIGN) was employed, utilizing similarity matrices for both amino acids and secondary structures.

    • Main Results:

    • STRALIGN achieved identical alignments to primary sequence-only methods for proteins with >45% primary sequence similarity.
    • Alignment accuracy significantly improved for proteins with lower primary sequence similarity.
    • For a protein pair with 16% primary sequence similarity, STRALIGN improved alignment from 0% to 37% 'correct' alignment.

    Conclusions:

    • The integration of secondary structure information into protein sequence comparison enhances alignment accuracy.
    • STRALIGN is a valuable tool for analyzing distantly related protein families, including globins, cytochrome c, and picornaviruses.