Genotype abbreviations

Creg Burns Darby cdarby at leland.Stanford.EDU
Sat Sep 11 14:17:57 EST 1999


For E. coli, the comprehensive reference is Escherichia coli and
Salmonella, Frederick Neidhardt, ed., 2nd edition, ASM Press, Washington.,
D.C., 1996.

Many of the genotypes for common E. coli strains are listed and explained
in the New England Biolabs catalog, which has a very handy reference
section.

As for the literature: Many of these genotypes, for example recA and lacZ,
are such common knowledge that they are omitted in most papers. For the
more obscure ones, authors tend to omit explanations unless the genotype
is directly relevant to their experiments. Tight space constraints in
journals make this practice necessary, but it does make the reading
harder for newcomers. 

Creg Darby					lab: 650-723-2671
Department of Microbiology and Immunology	fax: 650-723-1837
299 Campus Drive                                cdarby at stanford.edu
Stanford University Medical School		
Stanford, CA 94305

klaus_frommerr at my-deja.com writes:

>Hello!

>In microbiology you often encounter abbreviations - for restriction
>enzymes, for resistance genes and other genes. Whereas a list of
>restriction enzymes with their abbreviations can be found in lots of
>literature, I was not able to find such a list for genes and their
>abbreviations.

>For example the (mutation) genotype of the E. coli strain JM109 is
>indicated as follows:

>JM109  endA1, recA1, gyrA96, thi1, hsdR17(rk-,mk+), relA1, supE44,
>delta(proAB, lac), F'[proAB, laclq, lacZ(deltaM15), traD]

>Unfortunately I could not use the appropriate formatting (italics,
>sub-/superscript, greek letters) here. But I think you can read it
>anyway.

>Some of the abbreviations are easy to be guessed. But I do not know all
>of them. I have to know the strain's phenotypic traits, so I should know
>what all the abbreviations mean and how they affect metabolism or other
>processes in the strain.
>So does anybody know where I can look up for this sort of abbrevations?

>Note: Explaining the abbreviations in the above strain would help me a
>little, but I would prefer a reference to where I can find a list of
>this kind of abbreviations because the JM109 strain is just an example
>and I have others strain with other abbreviations.

>I wonder why they do not explain these abbreviations in most literature.
>Is an experienced microbiologist (which I am not) expected to know them?
>If yes, where did he/she learn about them?


>Klaus Frommer


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>Share what you know. Learn what you don't.
-- 
Creg Darby					lab: 650-723-2671
Department of Microbiology and Immunology	fax: 650-723-1837
299 Campus Drive                                cdarby at stanford.edu
Stanford University Medical School		
Stanford, CA 94305



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