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Updated: Jun 25, 2025

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Family-Free Genome Comparison
Marilia D V Braga1, Daniel Doerr2, Diego P Rubert3
1Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
None:
The comparison of large-scale genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC that, relying on built-in interfaces with a sequence comparison tool (either BLAST+ or DIAMOND) and with an ILP solver (either CPLEX or Gurobi), provides several methods for analyses that do not require prior classification of genes across the studied genomes. Taking annotated genome sequences as input, FFGC is a complete workflow for genome comparison allowing not only the computation of measures of similarity and dissimilarity but also the inference of gene families, simultaneously based on sequence similarities and large-scale genomic features.
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