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Related Experiment Videos

In silico sequence evolution with site-specific interactions along phylogenetic trees.

Tanja Gesell1, Arndt von Haeseler

  • 1Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1 40225 Duesseldorf, Germany.

Bioinformatics (Oxford, England)
|December 8, 2005
PubMed
Summary

This study introduces a new Markov model for nucleotide sequence evolution that accounts for site-specific interactions. The developed software, SISSI, enables versatile simulations of sequence evolution with complex dependencies.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Traditional models of sequence evolution do not account for dependencies between sites.
  • Biological sequences often exhibit complex interdependencies affecting their evolution.

Purpose of the Study:

  • To introduce a universal Markov model for nucleotide sequence evolution incorporating site-specific dependencies.
  • To develop a versatile tool for simulating sequence evolution with complex interactions.

Main Methods:

  • Developed a Markov model based on neighbourhood systems to describe site dependencies.
  • Created the Simulating Site-Specific Interactions (SISSI) program for sequence evolution simulations.
  • Implemented the model in ANSI C for cross-platform compatibility (UNIX/Linux, Windows, Mac OS).

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Main Results:

  • Demonstrated the ability to define and simulate complex models with site-specific interactions.
  • Successfully simulated RNA evolution, including secondary and tertiary structures (pseudoknots).
  • The SISSI program facilitates simulations of nucleotide and other character-based sequence evolution.

Conclusions:

  • The new model and SISSI program offer a versatile resource for studying sequence evolution with complex inter-site dependencies.
  • The method is applicable to various biological sequences and interaction types.
  • SISSI is publicly available for researchers to simulate complex evolutionary scenarios.