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Cyanorak v2.1 : a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

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Garczarek, Laurence, Guyet, Ulysse, Doré, Hugo, Farrant, Gregory K., Hoebeke, Mark, Brillet-Guéguen, Loraine, Bisch, Antoine, Ferrieux, Mathilde, Siltanen, Jukka, Corre, Erwan et al.
(2021) Cyanorak v2.1 : a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Research, 49 (D1). D667-D676. doi:10.1093/nar/gkaa958

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Official URL: https://doi.org/10.1093/nar/gkaa958

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Abstract

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
Q Science > QR Microbiology
Divisions: Faculty of Science > Life Sciences (2010- )
SWORD Depositor: Library Publications Router
Library of Congress Subject Headings (LCSH): Cyanobacteria , Microorganisms -- Motility, Photosynthetic bacteria , Gene mapping -- Data processing
Journal or Publication Title: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
ISSN: 1362-4962
Official Date: 8 January 2021
Dates:
DateEvent
8 January 2021Published
30 October 2020Available
28 October 2020Accepted
Volume: 49
Number: D1
Page Range: D667-D676
DOI: 10.1093/nar/gkaa958
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
ANR-13-ADAP-0010[ANR] Agence Nationale de la Recherchehttp://dx.doi.org/10.13039/501100001665
ANR17-CE2-0014-01[ANR] Agence Nationale de la Recherchehttp://dx.doi.org/10.13039/501100001665
ANR-11-INBS-0013[ANR] Agence Nationale de la Recherchehttp://dx.doi.org/10.13039/501100001665
NE/I00985X/1[NERC] Natural Environment Research Councilhttp://dx.doi.org/10.13039/501100000270
287589Seventh Framework Programmehttp://dx.doi.org/10.13039/100011102
11975Seventh Framework Programmehttp://dx.doi.org/10.13039/100011102
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