Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.
Garczarek, L
Guyet, U
Doré, H
Farrant, GK
Hoebeke, M
Brillet-Guéguen, L
Bisch, A
Ferrieux, M
Siltanen, J
Corre, E
Le Corguillé, G
Ratin, M
Pitt, FD
Ostrowski, M
Conan, M
Siegel, A
Labadie, K
Aury, J-M
Wincker, P
Scanlan, DJ
Partensky, F
- Publisher:
- Oxford University Press (OUP)
- Publication Type:
- Journal Article
- Citation:
- Nucleic acids research, 2020
- Issue Date:
- 2020-10-30
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Full metadata record
Field | Value | Language |
---|---|---|
dc.contributor.author | Garczarek, L | |
dc.contributor.author | Guyet, U | |
dc.contributor.author | Doré, H | |
dc.contributor.author | Farrant, GK | |
dc.contributor.author | Hoebeke, M | |
dc.contributor.author | Brillet-Guéguen, L | |
dc.contributor.author | Bisch, A | |
dc.contributor.author | Ferrieux, M | |
dc.contributor.author | Siltanen, J | |
dc.contributor.author | Corre, E | |
dc.contributor.author | Le Corguillé, G | |
dc.contributor.author | Ratin, M | |
dc.contributor.author | Pitt, FD | |
dc.contributor.author |
Ostrowski, M https://orcid.org/0000-0002-4357-3023 |
|
dc.contributor.author | Conan, M | |
dc.contributor.author | Siegel, A | |
dc.contributor.author | Labadie, K | |
dc.contributor.author | Aury, J-M | |
dc.contributor.author | Wincker, P | |
dc.contributor.author | Scanlan, DJ | |
dc.contributor.author | Partensky, F | |
dc.date.accessioned | 2020-11-17T02:34:21Z | |
dc.date.available | 2020-10-28 | |
dc.date.available | 2020-11-17T02:34:21Z | |
dc.date.issued | 2020-10-30 | |
dc.identifier.citation | Nucleic acids research, 2020 | |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issn | 1362-4962 | |
dc.identifier.uri | http://hdl.handle.net/10453/144079 | |
dc.description.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. | |
dc.format | Print-Electronic | |
dc.language | eng | |
dc.publisher | Oxford University Press (OUP) | |
dc.relation | Natural Environment Research CouncilNE/I00985X/1 | |
dc.relation.ispartof | Nucleic acids research | |
dc.relation.isbasedon | 10.1093/nar/gkaa958 | |
dc.rights | ©The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), whichpermits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | |
dc.rights | info:eu-repo/semantics/restrictedAccess | |
dc.subject | 05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences | |
dc.subject.classification | Developmental Biology | |
dc.title | Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. | |
dc.type | Journal Article | |
utslib.location.activity | England | |
utslib.for | 05 Environmental Sciences | |
utslib.for | 06 Biological Sciences | |
utslib.for | 08 Information and Computing Sciences | |
pubs.organisational-group | /University of Technology Sydney/Faculty of Science | |
pubs.organisational-group | /University of Technology Sydney/Strength - C3 - Climate Change Cluster | |
pubs.organisational-group | /University of Technology Sydney | |
utslib.copyright.status | recently_added | * |
dc.date.updated | 2020-11-17T02:34:17Z | |
pubs.publication-status | Published |
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.
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