CGG toolkit : Software components for computational genomics

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.

Karapiperis, ChristosAristotle University of Thessaloniki,Center for Research and Technology Hellas (author)
Baltsavia, IsminiUniversity of Crete (author)
Chasapi, AnastasiaCenter for Research and Technology Hellas (author)
Ahrén, DagLund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Bioinformatik,Forskargrupper vid Lunds universitet,Molecular Cell Biology,Department of Biology,Faculty of Science,Bioinformatics,Lund University Research Groups(Swepub:lu)mbek-dah (author)
Janssen, Paul J.Belgian Nuclear Research Centre (author)
Iliopoulos, IoannisUniversity of Crete (author)
Promponas, Vasilis J.University of Cyprus (author)
Enright, Anton J.University of Cambridge (author)
Ouzounis, Christos A.Center for Research and Technology Hellas,Aristotle University of Thessaloniki (author)
Center for Research and Technology HellasAristotle University of Thessaloniki (creator_code:org_t)

By the author/editor: Vasileiou, Dimit ...; Karapiperis, Chr ...; Baltsavia, Ismin ...; Chasapi, Anastas ...; Ahrén, Dag; Janssen, Paul J.; show more...; Iliopoulos, Ioan ...; Promponas, Vasil ...; Enright, Anton J ...; Ouzounis, Christ ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

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