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News/GMOD Paper Cuts, Nov 15th, 2013

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GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations [1]

The Aspergillus Genome Database (AspGD) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community.

A redesigned website and expanded resources for AspGD, which is now using JBrowse as primary genome browser.


CottonGen: a genomics, genetics and breeding database for cotton research [2]

CottonGen is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton.

An update on the CottonGen database, which uses the Tripal framework to make available data from a Chado database, and to integrate the GMOD tools GBrowse and CMap.


WormBase 2014: new views of curated biology [3]

WormBase is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans.

Updates and expansions on the WormBase website, which is notable not only for developing and using a number of GMOD tools, including GBrowse and Textpresso, but also for being hosted entirely in the cloud.


Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. [4]

The yeast Saccharomyces boulardii is used worldwide as a probiotic to alleviate the effects of several gastrointestinal diseases and control antibiotics-associated diarrhea. While many studies report the probiotic effects of S. boulardii, no genome information for this yeast is currently available in the public domain. We report the 11.4 Mbp draft genome of this probiotic yeast.

The newly-sequenced Saccharomyces boulardii genome, which was annotated with using MAKER.


DOOR 2.0: presenting operons and their functions through dynamic and integrated views [5]

We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009.

A bright, lively update to the Database of prokaryotic operons, which uses JBrowse for sequence visualization.


And finally, if you have access to the Wiley Online Library through your institution, you may like to check out [http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0915s43/abstract Cloud Computing with iPlant Atmosphere], from Current Protocols in Bioinformatics, which details the resources available on the [www.iplantcollaborative.org/‎ iPlant website] and how to get started with tools such as GBrowse.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1029
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1064
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1063
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1757-4749-5-30
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1048
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/15