I have a very long list of prokaryote organism names. I would like to know their gram staining (gram positive or gram negative) information.

Please let me know if there is any database that keeps this information.

I am also trying to find a program that can find gram staining information via organism name only as my organism list is long.

Edit: for each species the NCBI taxonomy lineage is also available

  • $\begingroup$ You only have their names, or you also have their genomes? $\endgroup$
    – mgalardini
    Aug 31 '17 at 13:13
  • $\begingroup$ I have only their names, I can able find their taxonomy lineage using NCBI taxonomy database if that helps me to find the gram staining. $\endgroup$ Aug 31 '17 at 13:26

The GOLD database can be used to retrieve a list of species names according to their Gram staining: go to the "Advanced search" page and select the either "gram-" or "gram+" under "Organism Fields" -> "Gram Stain". Then on the results page click on the number under "Organisms". On the results page you can select to have 1000 results per page, meaning that you would need to do some manual work.

I should add that as far as I know this information is based on what people submit when they register their genome projects, so I wouldn't expect this list to be curated or 100% accurate.

If you have access to the genome of the species you are interested in (you could download a representative strain for each species using ncbi-genome-download), you could use traitar, which can predict the gram staining, among other interesting broad phenotypes.

  • $\begingroup$ Thanks for your help. I was thinking about downloading GOLD database data and use a program to find my required information. But I am unable to download the data. So can you please help me to do that. $\endgroup$ Aug 31 '17 at 18:14
  • $\begingroup$ Is there any way to query the GOLD database programatically? $\endgroup$
    – llrs
    Sep 1 '17 at 7:25
  • 1
    $\begingroup$ No, their usage policy is in fact quite strict: "Downloading GOLD metadata by any means including web searches, downloadable reports, screen scraping, etc., is strictly prohibited without prior permission, if the purpose is to dissect, alter and store the GOLD data in a database (relational or text) and distribute to third parties/general public/collaborators." $\endgroup$
    – mgalardini
    Sep 1 '17 at 8:20

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