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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Family-Free Genome Comparison.

Daniel Doerr1, Pedro Feijão2,3, Jens Stoye4

  • 1School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)
|December 27, 2017
PubMed
Summary

Genome comparison reveals species phylogeny and organization using the family-free genome comparison tool (FFGC). This tool analyzes gene order without needing prior evolutionary knowledge, simplifying comparative genomics.

Keywords:
Common intervalsConserved adjacenciesDouble-cut-and-joinGene family-freeGene order analysisGenome distanceGenome similarity

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Genome structure comparison aids understanding of species phylogeny, genome organization, and gene associations.
  • Comparative genomics is crucial for evolutionary and functional insights.

Purpose of the Study:

  • To review the family-free genome comparison tool (FFGC).
  • To highlight FFGC's capabilities in gene order analysis without prior evolutionary relationship knowledge.
  • To present FFGC as a comprehensive workflow for genome comparison using only annotated genome sequences.

Main Methods:

  • Review of the FFGC tool and its methodologies.
  • Description of family-free gene order analysis techniques.
  • Explanation of the FFGC workflow from input to output.

Main Results:

  • FFGC offers multiple methods for gene order analysis.
  • FFGC does not require pre-existing knowledge of gene evolutionary relationships.
  • FFGC provides a complete genome comparison workflow.

Conclusions:

  • FFGC is a versatile tool for comparative genomics.
  • The tool simplifies genome comparison by eliminating the need for prior evolutionary data.
  • FFGC facilitates the study of genome organization and gene associations across species.