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CASS: Protein sequence simulation with explicit genotype-phenotype mapping

Johan A. Grahnen, David A. Liberles
  • Johan A. Grahnen
    Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
  • David A. Liberles
    Department of Molecular Biology, University of Wyoming, Laramie, WY, United States | liberles@uwyo.edu

Abstract

CASS (coarse-grained artificial sequence simulator) is a software package for simulating protein sequences with an explicit genotype-to-phenotype mapping that takes protein structure and function into account. It is capable of reproducing many structure-specific properties of protein sequence evolution, most notably spatial and temporal variation in rates, and has been used to investigate several hypotheses about the influence of thermodynamics on molecular evolution. The software is implemented in object-oriented C++, is supported on Linux, and the source code is made freely available under the GPL v3 license at http://www.wyomingbioinformatics.org/Liberle sGroup/CASS/.

Keywords

sequence-structure-function relationship, simulation, molecular evolution

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Submitted: 2012-07-13 09:00:19
Published: 2012-11-13 18:22:15
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Copyright (c) 2012 Johan A. Grahnen, David A. Liberles

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