CGG toolkit: Software components for computational genomics

• Published in: PLoS computational biology Vol. 19; no. 11; p. e1011498
• Main Authors: Vasileiou, Dimitrios, Karapiperis, Christos, Baltsavia, Ismini, Chasapi, Anastasia, Ahrén, Dag, Janssen, Paul J, Iliopoulos, Ioannis, Promponas, Vasilis J, Enright, Anton J, Ouzounis, Christos A
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 07.11.2023; Public Library of Science (PLoS)
• Subjects: Annotations; Archives & records; Availability; Bioinformatics; Bioinformatics (Computational Biology); Bioinformatik (beräkningsbiologi); Biology and Life Sciences; Clustering; Computational biology; Computer and Information Science; Computer and Information Sciences; Computer applications; Computer programs; Data collection; Data- och informationsvetenskap (Datateknik); Engineering and Technology; Funding; Genomes; Genomics; Infrastructure; Methods; Natural Sciences; Naturvetenskap; Proteins; R&D; Research & development; Research and Analysis Methods; Science; Software; Software utilities; Technology application; Toolkits; Greece
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1011498

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.