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Pooled CRISPR-Based Genetic Screens in Mammalian Cells
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gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution.

Sébastien Moretti1, Riccardo Murri, Sergio Maffioletti

  • 1Department of Ecology and Evolution, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Studies in Health Technology and Informatics
|September 4, 2012
PubMed
Summary
This summary is machine-generated.

Investigating genetic changes in species adaptation is complex. A new tool, gcodeml, uses Grid computing to analyze large phylogenetic datasets, aiding evolutionary studies.

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • Genomics

Background:

  • Understanding species adaptation requires analyzing genetic changes in protein-coding genes.
  • This analysis is computationally intensive, necessitating high-performance computing solutions.
  • Existing methods struggle with the scale of large phylogenetic datasets.

Purpose of the Study:

  • To develop an efficient computational tool for analyzing genetic changes related to species adaptation.
  • To leverage Grid and cluster computing for large-scale phylogenetic data analysis.
  • To provide a customizable solution for complex biological and scientific problems.

Main Methods:

  • Development of a Grid-enabled tool named gcodeml.
  • Utilization of the PAML (codeml) package for phylogenetic analysis.
  • Implementation on Grid and computational cluster environments.

Main Results:

  • gcodeml facilitates the analysis of large phylogenetic datasets.
  • The tool addresses the computational challenges in evolutionary studies.
  • The approach demonstrates applicability to diverse scientific domains.

Conclusions:

  • The gcodeml tool offers an efficient solution for studying genetic adaptation.
  • Grid and cluster computing are essential for tackling complex biological questions.
  • The developed methodology is adaptable for broader scientific applications.