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Protocols

CYORF specifications

Information


Unique identifier OMICS_22553
Name CYORF
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Kae Morishima
  • person_outline Miho Furumichi
  • person_outline Tatsuo Omata
  • person_outline Masahiko Ikeuchi

Publication for CYORF

CYORF citations

 (4)
library_books

Differential NtcA Responsiveness to 2 Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus

2018
Front Microbiol
PMCID: 5767323
PMID: 29375510
DOI: 10.3389/fmicb.2017.02641

[…] Selected cyanobacterial ntcA sequences were retrieved from CYORF (http://cyano.genome.jp/), Cyanobase (http://genome.microbedb.jp/cyanobase/), Integrated Microbial Genomes (https://img.jgi.doe.gov) and NCBI (http://www.ncbi.nlm.nih.gov/) databases. Protein BL […]

call_split

Physiological Studies of Glutamine Synthetases I and III from Synechococcus sp. WH7803 Reveal Differential Regulation

2016
Front Microbiol
PMCID: 4923085
PMID: 27446010
DOI: 10.3389/fmicb.2016.00969
call_split See protocol

[…] All available cyanobacterial glnA and glnN sequences were retrieved from CYORF, Cyanobase, Integrated Microbial Genomes, and NCBI databases. Molecular weight and pI values of the corresponding GS subunits were calculated using the tool compute pI/MW from ExPASy. Alignment […]

library_books

Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES 39

2010
PMCID: 2853384
PMID: 20203057
DOI: 10.1093/dnares/dsq004

[…] tein signature database, InterPro, were searched to assign the predicted protein sequences based on sequence similarities. Orthologous genes among cyanobacteria were manually curated using Gclust and CYORF. The KEGG database was used for pathway reconstruction. Signal peptides in proteins were predicted using SignalP, and transmembrane helices were predicted using TMHMM. […]

library_books

Glucose Uptake and Its Effect on Gene Expression in Prochlorococcus

2008
PLoS One
PMCID: 2565063
PMID: 18941506
DOI: 10.1371/journal.pone.0003416

[…] ication reactions ). Primers were designed utilizing the Oligo v. 4.05 software (Molecular Biology Insights), on the basis of the Prochlorococcus SS120 genome (whose sequences were retrieved from the CYORF database, available at http://cyano.genome.ad.jp/). The primers are described in .The amplification protocol was optimized to ensure that a single amplification product was obtained. This was mo […]

Citations

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CYORF institution(s)
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan; Fujitsu Kyushu System Engineering Limited, Fukuoka, Japan; Graduate School of Bioagricultural Sciences , Nagoya University, Nagoya, Japan; Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan

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