CGG toolkit: Software components for computational genomics

Dimitrios Vasileiou, Christos Karapiperis, Ismini Baltsavia, Anastasia Chasapi, Dag Ahrén, Paul Janssen, Ioannis Iliopoulos, Vasilis J. Promponas, Anton J. Enright, Christos A. Ouzounis

Research outputpeer-review


Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.

Original languageEnglish
Article numbere1011498
Number of pages10
JournalPLoS Computational Biology
Issue number11
StatePublished - 7 Nov 2023

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Modelling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

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