Family-Free Genome Comparison.
Common intervals
Conserved adjacencies
Double-cut-and-join
Gene family-free
Gene order analysis
Gene orthology inference
Genome distance
Genome median
Genome similarity
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
31
5
2024
pubmed:
31
5
2024
entrez:
31
5
2024
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 38819556
doi: 10.1007/978-1-0716-3838-5_3
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
57-72Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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