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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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COMPASS: the COMPletely Arbitrary Sequence Simulator.

Andrew Low1, Nicolas Rodrigue1, Alex Wong1

  • 1Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6.

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|June 6, 2017
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Summary
This summary is machine-generated.

Bioinformatics tools can now be tested with simulated sequence alignments using the new COMPASS simulator. COMPASS allows for the evolution of any discrete state space, overcoming limitations of previous tools.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Simulated sequence alignments are crucial for evaluating bioinformatics tools.
  • Existing sequence simulators are restricted to predefined state spaces.
  • There is a need for more flexible sequence simulation methods.

Purpose of the Study:

  • To introduce a novel sequence simulator, COMPASS (COMPletely Arbitrary Sequence Simulator).
  • To enable simulation of sequence evolution across any discrete state space.
  • To support any time-reversible model for evolutionary simulations.

Main Methods:

  • COMPASS simulates sequence evolution along a phylogenetic tree.
  • It accommodates arbitrary discrete state spaces.
  • It supports any time-reversible model.

Main Results:

  • COMPASS overcomes the state-space limitations of current sequence simulators.
  • It provides a flexible platform for simulating diverse evolutionary scenarios.
  • The tool facilitates robust testing of bioinformatics software.

Conclusions:

  • COMPASS significantly advances the capabilities of sequence simulation.
  • It offers unprecedented flexibility for modeling evolutionary processes.
  • This tool will enhance the development and validation of bioinformatics algorithms.