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CyanoBase specifications

Information


Unique identifier OMICS_03180
Name CyanoBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Yasukazu kamura

Publications for CyanoBase

CyanoBase citations

 (52)
library_books

Draft Genome Sequence of the Nitrogen Fixing and Hormogonia Inducing Cyanobacterium Nostoc cycadae Strain WK 1, Isolated from the Coralloid Roots of Cycas revoluta

2018
Genome Announc
PMCID: 5814485
PMID: 29449379
DOI: 10.1128/genomeA.00021-18

[…] using a BLAST search. Finally, we obtained 68 cyanobacterium-derived scaffolds with high similarity to the genus Nostoc. Gene annotation was performed by MiGAP () and by manual curation referring to CyanoBase (, ).The total length of the draft genome sequence of N. cycadae strain WK-1 without gap regions was 6,773,844 bp, with a G+C content of 39.06%. Of the total predicted genes, 5,465 coding se […]

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 BLAST analysis were performed using […]

library_books

Edible Cyanobacterial Genus Arthrospira: Actual State of the Art in Cultivation Methods, Genetics, and Application in Medicine

2017
Front Microbiol
PMCID: 5741684
PMID: 29326676
DOI: 10.3389/fmicb.2017.02541

[…] ., ). In the study of Zhao et al. (), Synechocystis, Synechococcus Prochlorococcus, Anabaena, Nostoc, Spirulina, and Trichodesmium strains were examined in silico, using the RM gene set obtained from CyanoBase. The (BLAST)P and TBLASTN tools were used to obtain 30 putative RM genes, mostly type I RM systems. Additionally, gene expression profiles for “Spirulina” methyltransferases were characteriz […]

library_books

A Carbon Dioxide Limitation Inducible Protein, ColA, Supports the Growth of Synechococcus sp. PCC 7002

2017
Mar Drugs
PMCID: 5742850
PMID: 29244744
DOI: 10.3390/md15120390

[…] tained from CyanoBase (http://genome.microbedb.jp/CyanoBase) [].To construct the phylogenetic tree of gene homologs for ColA, we searched for gene homologs among cyanobacteria using the BLAST tool in CyanoBase. Amino acid sequences of these gene products were aligned in ClustalW []. The evolutionary history of these genes was inferred using the neighbor-joining method []. The percentages of replic […]

library_books

Minimal tool set for a prokaryotic circadian clock

2017
BMC Evol Biol
PMCID: 5520375
PMID: 28732467
DOI: 10.1186/s12862-017-0999-7

[…] in sequences of the 23 clock related proteins (Additional file : Table S1), from Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, respectively, were checked against the entries in the Cyanobase Database to ensure correctness [] (version May 2016). These 23 protein sequences were used as queries for a search of homologs within the custom protein database, applying the standalone ver […]

call_split

Exploring Components of the CO2 Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome Based Analysis

2017
Comput Struct Biotechnol J
PMCID: 5472144
PMID: 28652895
DOI: 10.1016/j.csbj.2017.05.001
call_split See protocol

[…] d NATL2A, and Prochlorococcus marinus MIT 9211, 9215, 9301, 9303, 9312, 9313, and 9515) cyanobacteria. Their corresponding amino acid sequences were retrieved from the public databases, including the CyanoBase (http://genome.kazusa.or.jp/cyanobase) and the GenBank (http://www.ncbi.nlm.nih.gov/genbank) databases. A phylogenetic tree was created by performing multiple sequence alignment with MUSCLE […]

Citations

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CyanoBase institution(s)
Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan; Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan; Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan; NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan; Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan; Graduate School of Horticulture, Chiba University, Matsudo, Japan; Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan; Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
CyanoBase funding source(s)
Integrated Database Project, Ministry of Education, Culture, Sports, Science and Technology of Japan, National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).

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