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Related Experiment Videos

Mocca: semi-automatic method for domain hunting.

C Notredame1

  • 1Information Genetique et Structurale, CNRS-UMR 1889, 31 Ch. Joseph Aiguier, 13 402 Marseille, France.

Bioinformatics (Oxford, England)
|April 13, 2001
PubMed
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Multiple Occurrences Analysis (Mocca) is a novel repeat extraction method. It efficiently identifies homologous sequence segments, aiding in protein domain hunting and repeat analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Existing methods for repeat extraction can be limited in scope and efficiency.
  • Identifying and analyzing protein repeats is crucial for understanding protein function and evolution.

Purpose of the Study:

  • To introduce Multiple Occurrences Analysis (Mocca), a new method for efficient repeat extraction.
  • To provide a tool for domain hunting and interactive analysis of protein repeats.

Main Methods:

  • Mocca is based on the T-Coffee package.
  • It extracts sequence segments homologous to a master sequence using a library of local alignments.
  • The method is optimized for speed and ease of use in interactive analysis.

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Main Results:

  • Mocca successfully extracts homologous sequence segments.
  • The method is effective for domain hunting and analyzing protein repeats.
  • It handles highly divergent protein repeats (less than 30% amino acid identity) and segments longer than 30 amino acids.

Conclusions:

  • Mocca offers a fast and user-friendly approach for identifying and analyzing protein repeats.
  • This method facilitates the testing of new boundaries and the extension of known repeats.
  • Mocca is particularly valuable for studying highly divergent and long protein repeats.