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T2prhd: a tool to study the patterns of repeat evolution.

Botond Sipos1, Kálmán Somogyi, István Andó

  • 1Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, P.O. Box 521, H-6701 Szeged, Hungary. sbotond@gmail.com

BMC Bioinformatics
|January 22, 2008
PubMed
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We developed a novel visual method to study sequence repeat evolution, considering exact repeat positions. This tool, t2prhd, aids in understanding gene family evolution and repeat patterns.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Evolutionary models like birth-and-death and concerted models are used for multigene families and sequence repeats.
  • Phylogenetic reconstruction is key for studying gene family and sequence repeat evolution.
  • Accurate characterization requires considering sequence repeat positions, not just order.

Purpose of the Study:

  • To develop a rapid visual approach for studying sequence repeat evolution.
  • To incorporate exact repeat positions into the analysis of sequence repeats.
  • To provide a user-friendly tool for assessing repeat evolution patterns.

Main Methods:

  • Developed a novel rapid visual approach for repeat evolution analysis.
  • Utilized pairwise repeat homology diagrams to visualize sequence repeats and homology.

Related Experiment Videos

  • Employed profile hidden Markov models (HMMs) for repeat detection and phylogenetic trees for homology inference.
  • Implemented the method in a Perl script (t2prhd) with command-line and online interfaces.

    • Main Results:

    • The pairwise repeat homology diagram method visualizes repeats and their homology relations.
    • The t2prhd tool effectively analyzes repeat evolution, demonstrated on EGF-like and fibronectin-III-like domain repeats in Tenascin sequences.
    • The method allows for rapid and intuitive assessment of repeat evolution.

    Conclusions:

    • Pairwise repeat homology diagrams offer a quick and intuitive way to assess repeat evolution.
    • The t2prhd tool is valuable for studying repeat evolution patterns, especially in large datasets.
    • The command-line interface facilitates automated generation of diagrams for large-scale analyses.