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A symmetric-iterated multiple alignment of protein sequences

L Brocchieri1, S Karlin

  • 1Department of Mathematics, Stanford University, CA 94305-2125, USA.

Journal of Molecular Biology
|March 26, 1998
PubMed
Summary

A novel iterative method aligns protein sequences by combining motif finding and dynamic programming. This approach reveals conserved blocks in RecA-like proteins, aiding functional and evolutionary analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Multiple sequence alignment is crucial for understanding protein function and evolution.
  • Existing methods may struggle with large datasets or complex evolutionary relationships.

Purpose of the Study:

  • To introduce a new symmetric-iterative method for multiple protein sequence alignment.
  • To enhance the analysis of protein families, including functional and evolutionary insights.

Main Methods:

  • Combines motif finding and dynamic programming.
  • Utilizes a significant segment pair alignment (SSPA) protocol.
  • Iterative consensus sequence construction with differential weighting.

Main Results:

  • Identified eleven conserved blocks in RecA-like sequences, including ATP-binding sites.
  • Revealed distinct alignments for eubacterial RecA and eukaryotic/archaeal Rad51/RadA.
  • Highlighted conserved glycine and charged/polar residues, suggesting roles in structure and interactions.

Conclusions:

  • The method effectively aligns protein sequences, accommodating indels and variable unaligned segments.
  • Conserved blocks and residue analysis provide insights into RecA/Rad51 filament formation and interactions.
  • The approach is valuable for database searches and comparative analysis of protein families.

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