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BsubCyc Update History

This document summarizes the history of updates to BsubCyc.

Release Notes for BsubCyc Version 2.5

Released on March 24, 2014.

The computational GO term assigments have been updated with new data from UniProt.

BsubCyc now cites 334 publications from 2013 and 23 publications from 2014.

Release Notes for BsubCyc Version 2.4

Released on December 17, 2013.

BsubCyc now cites 303 publications from 2013.

Release Notes for BsubCyc Version 2.3

Released on October 11, 2013.

BsubCyc now cites 241 publications from 2013.

Release Notes for BsubCyc Version 2.2

Released on June 11, 2013.

BsubCyc now cites 134 publications from 2013.

Release Notes for BsubCyc Version 2.1

Released on March 28, 2013.

BsubCyc now cites 266 publications from 2012 and 50 publications from 2013.

Release Notes for BsubCyc Version 2.0

Released on November 14, 2012.

BsubCyc has been updated to add protein feature information from UniProt. In addition, we have added links to the Bacillus Genetic Stock Center from the gene/protein pages of many of the genes for which null mutant strains are available at the BGSC.

BsubCyc now cites 232 publications from 2012.

Release Notes for BsubCyc Version 1.9

Released on July 5, 2012.

BsubCyc now cites 328 publications from 2011 and 102 publications from 2012.

Release Notes for BsubCyc Version 1.8

Released on February 20, 2012.

We have added transcription units for all "single-gene directons" to BsubCyc. Single-gene directons are genes that are encoded on the opposite strand compared to both the upstream and downstream neighboring genes, and thus have to be transcribed as single-gene transcription units.

BsubCyc now cites 323 publications from 2011 and 10 publications from 2012.

Release Notes for BsubCyc Version 1.7

Released on October 21, 2011.

The last few months have seen a large number of publications where the functions of previously unknown genes have been identified. Short summaries of several function updates can be found on the main BsubCyc website.

BsubCyc now cites 221 publications from 2011 and 223 publications from 2010.

Release Notes for BsubCyc Version 1.6

Released on June 8, 2011.

Citations to recently published research articles are regularly being added to the genes/proteins that were studied. BsubCyc now contains 1935 literature references, including 119 references to papers published in 2011.

The final missing enzyme in the biosynthesis of queuosine, a base that replaces guanine in the wobble position of a subset of tRNAs, has been identified. Two new pathways, preQ0 biosynthesis and queuosine biosynthesis, show the series of biochemical steps that lead to the final modified tRNA product.

Release Notes for BsubCyc Version 1.5

Released on March 18, 2011.

In this release, we have corrected the accidental deletion of a number of Gene Ontology terms that had been imported from UniProt. BsubCyc should now contain the full complement of GO terms from UniProt, as well as GO terms with experimental evidence codes that were assigned based on recent publications.

Release Notes for BsubCyc Version 1.4

Released on December 3, 2010.

The major update for this release is the addition of Gene Ontology terms from UniProt. More than 29,000 GO term assignments, largely with computational evidence, were added to genes/proteins in BsubCyc. GO terms can be used to search for gene products with related function, involved in the same process, or residing in the same subcellular location.

Release Notes for BsubCyc Version 1.3

Released on October 1, 2010.

This is a minor release with a small number of changes; references to recent literature were added to a number of gene products.

Release Notes for BsubCyc Version 1.2

Released on August 20, 2010.

This is a minor release with a small number of changes:

  • We added links to GenoList (the successor of SubtiList), SubtilisWiki, and the STRING protein interaction network database to the gene/protein pages of BsubCyc.

  • Some improvements to the representation of riboswitches were made.

Release Notes for BsubCyc Version 1.1

Released on June 16, 2010.

Two major improvements to BsubCyc are included in this release:

  • We imported a large number of transcriptional regulatory interactions from the DBTBS database. You can now browse the transcriptional regulatory network of B. subtilis using the Tools > Regulatory Overview menu.

  • Ortholog data for B. subtilis is now available, enabling a number of comparative analysis operations. From each gene/protein page, you can select and display orthologs by selecting the "Align in Multi-Genome Browser" or "Compare Orthologs" buttons. Other comparative analysis tools can be accessed via the Tools > Comparative Analysis menu.

Release Notes for BsubCyc Version 1.0

Released on March 18, 2010.

This is the first release of the BsubCyc model-organism database for Bacillus subtilis. The database was built using the Pathway Tools software and is based on the sequence and annotation of the B. subtilis genome in Genbank record AL009126.3 GI:225184640, produced by the Genoscope group (Antoine Danchin), October 1, 2009. This Genbank record reflects the corrected nucleotide sequence and revised genome annotation published in Barbe et al. (2009).

Further improvements to the automatically-built database were made as follows:

  • Older gene name synonyms were added to the gene objects. Synonyms were obtained from the GenoList database.

  • We scanned the B. subtilis literature for genes that were renamed after the reannotation of the genome and added these gene names and the appropriate literature citations to BsubCyc.

  • Links to the SubtiWiki site were added to each gene/protein page.

We plan to further enhance the utility of BsubCyc by incorporating the following information in future releases:

  • DBTBS transcriptional regulatory data

  • UniProt Gene Ontology data

  • UniProt protein feature data

  • Data produced by the B. subtilis GO grant consortium