CGG toolkit : Software components for computational genomics
Vasileiou, Dimitrios ; Karapiperis, Christos ; Baltsavia, Ismini ; Chasapi, Anastasia ; Ahrén, Dag LU
; Janssen, Paul J.
; Iliopoulos, Ioannis
; Promponas, Vasilis J.
; Enright, Anton J.
and Ouzounis, Christos A.
(2023)
In PLoS Computational Biology
19(11).
- 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... (More)
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.
(Less)
- author
- Vasileiou, Dimitrios
; Karapiperis, Christos
; Baltsavia, Ismini
; Chasapi, Anastasia
; Ahrén, Dag
LU
; Janssen, Paul J.
; Iliopoulos, Ioannis
; Promponas, Vasilis J.
; Enright, Anton J.
and Ouzounis, Christos A.
- organization
- publishing date
- 2023-11
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS Computational Biology
- volume
- 19
- issue
- 11
- article number
- e1011498
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- pmid:37934729
- scopus:85176737355
- ISSN
- 1553-734X
- DOI
- 10.1371/journal.pcbi.1011498
- language
- English
- LU publication?
- yes
- id
- ebfc03bd-7029-4526-b3c4-83c0a97b547a
- date added to LUP
- 2024-01-04 16:35:38
- date last changed
- 2024-04-19 12:56:20
@article{ebfc03bd-7029-4526-b3c4-83c0a97b547a,
abstract = {{<p>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.</p>}},
author = {{Vasileiou, Dimitrios and Karapiperis, Christos and Baltsavia, Ismini and Chasapi, Anastasia and Ahrén, Dag and Janssen, Paul J. and Iliopoulos, Ioannis and Promponas, Vasilis J. and Enright, Anton J. and Ouzounis, Christos A.}},
issn = {{1553-734X}},
language = {{eng}},
number = {{11}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS Computational Biology}},
title = {{CGG toolkit : Software components for computational genomics}},
url = {{http://dx.doi.org/10.1371/journal.pcbi.1011498}},
doi = {{10.1371/journal.pcbi.1011498}},
volume = {{19}},
year = {{2023}},
}