CGG toolkit: Software components for computational genomics.

Vasileiou D, Karapiperis C, Baltsavia I, Chasapi A, Ahrén D, Janssen PJ, Iliopoulos I, Promponas VJ, Enright AJ, Ouzounis CA

PLoS Comput. Biol. 19 (11) e1011498 [2023-11-00; online 2023-11-07]

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.

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed 37934729

DOI 10.1371/journal.pcbi.1011498

Crossref 10.1371/journal.pcbi.1011498

pmc: PMC10629618
pii: PCOMPBIOL-D-23-00660

Publications 9.5.0