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MicrobeDB specifications

Information


Unique identifier OMICS_08271
Name MicrobeDB
Restrictions to use None
Database management system MySQL
Maintained Yes

Documentation


Maintainer


  • person_outline Morgan Langille

Publication for MicrobeDB

MicrobeDB citations

 (14)
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 NCBI BLASTp tool (http:/ […]

library_books

Transcriptomic Responses in the Bloom Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton

2017
Appl Environ Microbiol
PMCID: 5311399
PMID: 28003198
DOI: 10.1128/AEM.02832-16

[…] d clade-specific microbial marker genes. Differentially expressed genes were assigned functional categories based upon categories found in CyanoBase for the Microcystis NIES-843 genome (http://genome.microbedb.jp/cyanobase/GCA_000010625.1). Full differential expression results can be found in Table S1 to S6 in the supplemental material. Principal-component analysis (PCA) for functional category si […]

call_split

Comparison of aldehyde producing activities of cyanobacterial acyl (acyl carrier protein) reductases

2016
Biotechnol Biofuels
PMCID: 5090900
PMID: 27822307
DOI: 10.1186/s13068-016-0644-5
call_split See protocol

[…] ructed using 16S ribosomal RNA []. Multiple sequence alignment of 12 representative AARs was carried out using the Clustal X software [].The habitats of 128 cyanobacterial species were examined using MicrobeDB (http://microbedb.jp/), CyanoBase (http://genome.microbedb.jp/cyanobase/) [], and the Pasteur Culture collection of Cyanobacteria (PCC; http://cyanobacteria.web.pasteur.fr/). Sixty-nine and […]

library_books

The Evolution of Silicon Transport in Eukaryotes

2016
Mol Biol Evol
PMCID: 5100055
PMID: 27729397
DOI: 10.1093/molbev/msw209

[…] ely low similarity of the bacterial SIT-L sequences to SdSITa, the Synechococcus sp. KORDI-100 SIT-L was used as a query sequence for prokaryotic database searches, including Cyanobase (http://genome.microbedb.jp/cyanobase; last accessed October 12, 2016), Cyanorak (www.sb-roscoff.fr/cyanorak/; last accessed October 12, 2016), and the Tara Oceans metaG Environmental Sequence Datasets (0.22–8-μm fr […]

call_split

Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120

2016
J Exp Bot
PMCID: 4915528
PMID: 27012282
DOI: 10.1093/jxb/erw112
call_split See protocol

[…] , Finland). Significantly differentially expressed genes were identified using a false discovery rate (FDR: Benjamini–Hochberg) cutoff of 0.05. Gene descriptions were collected from Cyanobase (genome.microbedb.jp/cyanobase/) and KEGG (www.genome.jp/kegg/). […]

library_books

Investigation of a Quadruplex Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

2015
PLoS One
PMCID: 4692102
PMID: 26695179
DOI: 10.1371/journal.pone.0144275

[…] hboring ORF of 0–50 bp, 50–100 bp and > 100 bp. Functions of annotated genes and their positions on the genome were collected from KEGG (http://www.kegg.jp/), NCBI as well as Cyanobase (http://genome.microbedb.jp/cyanobase) []. Repeat associated genes were sorted into functional categories using the KEGG pathway mapper (http://www.genome.jp/kegg/mapper.html) []. […]

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MicrobeDB institution(s)
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada

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