TY - JOUR
T1 - CGG toolkit
T2 - Software components for computational genomics
AU - Vasileiou, Dimitrios
AU - Karapiperis, Christos
AU - Baltsavia, Ismini
AU - Chasapi, Anastasia
AU - Ahrén, Dag
AU - Janssen, Paul
AU - Iliopoulos, Ioannis
AU - Promponas, Vasilis J.
AU - Enright, Anton J.
AU - Ouzounis, Christos A.
N1 - Score= 10
Publisher Copyright:
© 2023 Vasileiou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2023/11/7
Y1 - 2023/11/7
N2 - 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.
AB - 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.
KW - Software tools
KW - Algorithms
KW - Sequence analysis
KW - Genome comparison
KW - Molecular phylogeny
KW - Protein-protein interactions
KW - Genetic networks
KW - Data unification
KW - Protein family databases
UR - http://www.scopus.com/inward/record.url?scp=85176737355&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1011498
DO - 10.1371/journal.pcbi.1011498
M3 - Article
C2 - 37934729
AN - SCOPUS:85176737355
SN - 1553-734X
VL - 19
JO - PLoS Computational Biology
JF - PLoS Computational Biology
IS - 11
M1 - e1011498
ER -