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Protocols

SubtiWiki specifications

Information


Unique identifier OMICS_02779
Name SubtiWiki
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 2.0
Maintained Yes

Taxon


  • Bacteria
    • Bacillus subtilis

Subtools


  • Expression Browser
  • Genome Browser
  • Interaction Browser
  • Pathway Browser
  • Regulation Browser

Maintainers


  • person_outline Jörg Stülke
  • person_outline Bingyao Zhu

Publications for SubtiWiki

SubtiWiki citations

 (10)
library_books

Dynamic sporulation gene co expression networks for Bacillus subtilis 168 and the food borne isolate Bacillus amyloliquefaciens: a transcriptomic model

2018
Microb Genom
PMCID: 5857382
PMID: 29424683
DOI: 10.1099/mgen.0.000157

[…] and differences in gene expression for groups of genes, especially those linked to sporulation. To benchmark the reconstructed networks, a list of genes in regulons of B. subtilis was downloaded from SubtiWiki (http://subtiwiki.uni-goettingen.de/) [] and SporeWeb [] and then mapped onto the GCN. File S2 and File S3 contain the data for the secondary network reconstruction corresponding to B. subti […]

call_split

T7 RNA polymerase‐driven inducible cell lysis for DNA transfer from Escherichia coli to Bacillus subtilis

2017
PMCID: 5658589
PMID: 28815907
DOI: 10.1111/1751-7915.12843
call_split See protocol

[…] d from the E. coli K‐12 project website (http://www.xbase.ac.uk/genome/escherichia-coli-str-k-12-substr-mg1655). The B. subtilis genome sequence was obtained from the BioCyc (http://bsubcyc.org/) and SubtiWiki (http://subtiwiki.uni-goettingen.de/) databases. The sequences of the parts (promoters, RBS, terminators) of the DNA constructs were obtained from the Registry of Standard Biological Parts ( […]

call_split

Combining Genes from Multiple Phages for Improved Cell Lysis and DNA Transfer from Escherichia coli to Bacillus subtilis

2016
PLoS One
PMCID: 5087902
PMID: 27798678
DOI: 10.1371/journal.pone.0165778
call_split See protocol

[…] are DNA sequences. E. coli K-12 project website (http://www.xbase.ac.uk/genome/escherichia-coli-str-k-12-substr-mg1655) was the source of the E. coli genome sequence. BioCyc (http://bsubcyc.org/) and SubtiWiki (http://subtiwiki.uni-goettingen.de/) databases were used to obtain the B. subtilis genome sequence. The sequences of DNA constructs were obtained from the Registry of Standard Biological Pa […]

call_split

Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High Salinity Environments Using RNA Sequencing

2016
Front Microbiol
PMCID: 5052260
PMID: 27766092
DOI: 10.3389/fmicb.2016.01564
call_split See protocol

[…] er et al., ). Hierarchical clustering of transcription profiles was performed with the TIGR Multiexperiment Viewer (MeV, http://mev.tm4.org/). Functional categorization was performed according to the SubtiWiki platform (http://www.subtiwiki.uni-goettingen.de; Mäder et al., ; Michna et al., ). The RNA-seq data was deposited in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/ […]

call_split

Lambda Red recombinase mediated integration of the high molecular weight DNA into the Escherichia coli chromosome

2016
Microb Cell Fact
PMCID: 5050610
PMID: 27716307
DOI: 10.1186/s12934-016-0571-y
call_split See protocol

[…] The B. subtilis genome sequence was obtained from the SubtiWiki (http://subtiwiki.uni-goettingen.de/) and BioCyc (http://bsubcyc.org/) databases. The E. coli K-12 MG1655 genome sequence was obtained from the E. coli K-12 project website (http://www.xbase […]

library_books

Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity

2016
PLoS One
PMCID: 4896439
PMID: 27272929
DOI: 10.1371/journal.pone.0156796

[…] gnment was made on te amino acid level using Muscle [] to facilitate identification of pseudogenes (encoding incomplete proteins).The carbohydrate utilization systems of B. subtilis 168 listed in the Subtiwiki database (highly curated) [] were initially used to search for orthologous systems in the B. cereus OG table. Additional genes and systems were found with keyword searches and genome context […]

Citations

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SubtiWiki institution(s)
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Gottingen, Gottingen, Germany
SubtiWiki funding source(s)
Supported by the Gottingen Center for Molecular Lifesciences.

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