I am looking for a database which I can use to programmatically mark the taxa in my project as either Gram +ve or Gram -ve. It looks like the NCBI used to maintain a file (lproks_0.txt) with this information but they no longer do. If anyone has a resource that I could use for this purpose I would appreciate the help.
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2 answers
For example:
GlobalRPH:
http://www.globalrph.com/bacterial-strains-background.htm
See also these posts:
Old version of NCBI had this information.
A: Bacterial morphology details
Bergey's Manual, as 5heikki said:
Is there a free database of bacterial phenotype information by species name?
Wiki, as genomax2 suggested:
List of gram negative bacteria
See these papers:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013690/
PSORTdb—an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea
https://en.wikipedia.org/wiki/Bacterial_taxonomy
and there go to Subdivisions based on Gram staining
The presentation describes the difference:
http://www.jove.com/science-education/10092/gram-staining-of-bacteria-from-environmental-sources
I found the R package AMR usefull to assign gram staining based on taxonomy. See mo_gramstain(x, language = get_AMR_locale(), ...)
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Gram Staining is procedure of identifying bacteria in General Laboratory uses. The Gram Stain Kit (Modified Brown & Brenn) is intended for the demonstration and differentiation of Gram-positive and Gram-negative bacteria.
Gram Positive Bacteria: Blue Gram Negative Bacteria: Red Other Tissue: Slightly Yellow - Pink Nuclei: Red http://scytek.com/products/33.35-BBS-2-Gram-Stain-Kit-(Modified-Brown-&-Brenn).asp