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Vasileiou D, Karapiperis C, Baltsavia I, Chasapi A, Ahrén D, Janssen PJ, Iliopoulos I, Promponas VJ, Enright AJ, Ouzounis CA. CGG toolkit: Software components for computational genomics. PLoS Comput Biol 2023; 19:e1011498. [PMID: 37934729 PMCID: PMC10629618 DOI: 10.1371/journal.pcbi.1011498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/07/2023] [Indexed: 11/09/2023] Open
Abstract
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.
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Affiliation(s)
- Dimitrios Vasileiou
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Christos Karapiperis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- Biological Computation & Computational Biology Group, AIIA Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, Greece
| | - Ismini Baltsavia
- Computational Biology Group, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Dag Ahrén
- Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden
| | - Paul J. Janssen
- Nuclear Medical Applications, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
| | - Ioannis Iliopoulos
- Computational Biology Group, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, Nicosia, Cyprus
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Christos A. Ouzounis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- Biological Computation & Computational Biology Group, AIIA Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, Greece
- SysBioBio.info (SBBI), Thessalonica, Greece
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Chasapi A, Aivaliotis M, Angelis L, Chanalaris A, Iliopoulos I, Kappas I, Karapiperis C, Kyrpides NC, Pafilis E, Panteris E, Topalis P, Tsiamis G, Vizirianakis IS, Vlassi M, Promponas VJ, Ouzounis CA. Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput Biol 2019; 15:e1007532. [PMID: 31856214 PMCID: PMC6922331 DOI: 10.1371/journal.pcbi.1007532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Anastasia Chasapi
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Michalis Aivaliotis
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessalonica, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Anastasios Chanalaris
- Botnar Research Centre, NDORMS, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
| | - Ilias Kappas
- School of Biology, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Christos Karapiperis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Eleftherios Panteris
- First Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - George Tsiamis
- Department of Environmental Engineering, School of Engineering, University of Patras, Patras, Greece
| | - Ioannis S. Vizirianakis
- Department of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail: (VJP); (CAO)
| | - Christos A. Ouzounis
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- * E-mail: (VJP); (CAO)
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Abstract
Bioinformatics plays a key role in supporting the life sciences. In this work, we examine bioinformatics in Jordan, beginning with the current status of bioinformatics education and research, then exploring the challenges of advancing bioinformatics, and finally looking to the future for how Jordanian bioinformatics research may develop.
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Affiliation(s)
- Qanita Bani Baker
- Department of Computer Science, Jordan University of Science and Technology, Irbid, Jordan
| | - Maryam S. Nuser
- Department of Computer Science, Jordan University of Science and Technology, Irbid, Jordan
- Department of Information Systems, Yarmouk University, Irbid, Jordan
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