Wednesday, September 06, 2006

GenBank extras

Idly playing with ants, it is time to blog two things that come up a few times. The first is that GenBank has links to literature that could do with updating. For example, the sequence U11912 from the fungus "Atta mexicana symbiont JF-1" is listed as being published in

AUTHORS Rehner,S.A., Chapela,I.H., Schultz,T.R. and Mueller,U.G.
TITLE Evolutionary history of the symbiosis between fungus-growing ants
and their fungi
JOURNAL Unpublished

Well, this was published in Science (doi:10.1126/science.266.5191.1691) in 1994. The DOI seems broken (sigh), so here is a direct link. Ulrich Mueller's web site has a link to the PDF.
The other point is that searching the nucleotide database for "Atta mexicana" turns up no ants, but the above mentioned fungus. We get the hit because there is a line in the GenBank record that lists the ant host.

/specific_host="Atta mexicana"

As I've mentioned over on the iSpecies blog, GenBank records often contain this sort of useful information. Hence, we could search for ants and extract information about their fungal associates.


  • Of course, this all assumes that people can spell, which clearly they can't. For example, AF491892 for "cf. Escherichia coli symbiont 1 of Acromyrmex octospinosus" (see doi:10.1186/1471-2148-2-9) has "Acromyrmex otcospinosus" as the specific host. Doh!

    By Blogger Rod Page, at 5:35 pm  

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