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xREI: a phylo-grammar visualization webserver.

Lars Barquist1, Ian Holmes

  • 1Department of Bioengineering, University of California, Berkeley, USA. lbarquist@gmail.com

Nucleic Acids Research
|June 5, 2008
PubMed
Summary
This summary is machine-generated.

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This study introduces xrate and xREI, tools simplifying the development and application of phylo-grammars for evolutionary analysis. These advancements facilitate the annotation and study of structured features in biological sequences.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylo-grammars integrate Markov models and stochastic grammars for sequence analysis.
  • Previous methods for phylo-grammar development were complex and time-consuming.

Purpose of the Study:

  • To present xrate for efficient phylo-grammar development and parameterization.
  • To introduce xREI, a web interface for visualizing and utilizing phylo-grammars.

Main Methods:

  • xrate utilizes a simple file format for rapid phylo-grammar creation.
  • Automated parameterization is achieved through the Expectation Maximization algorithm.
  • xREI provides an AJAX-based interface for grammar visualization and analysis.

Main Results:

Related Experiment Videos

  • xrate enables streamlined development and automated parameterization of phylo-grammars.
  • xREI offers intuitive grammar visualization and access to training/annotation functions.

Conclusions:

  • xrate and xREI significantly simplify the creation and application of phylo-grammars.
  • These tools are valuable for researchers developing and exploring evolutionary models.