help with nomenlature in S. pombe

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Thu Jan 18 15:03:50 EST 1996


Zhaomin Yang wrote:

> > I tried to figure out how the
> > genetic nomenclature works for S. pombe. It has been a totally
> > confusion.

SLForsburg <susan_forsburg at qm.salk.edu> wrote:
 
>                                           S. p
>  A wildtype locus                        * arg4+ (+ superscript)
>                          
>  A recessive or dom  allele             :* arg4- (ditto) or arg4
>  The wild-type allele                    * arg4+
>  A specific allele or mutation          * arg4-2
>  A strain that doesn't require arginine  Arg+ or arg+
>  A strain that requires arginine         Arg- or arg-
>  The protein encoded by the gene         Arg4p (or Arg4 or arg4)
>  
>                              * Italic


Susan (and other pombe friends),

I don't think it's very practical to have a system which requires
italic and lower/upper case!  

Would it not be more useful (read: easier to maintain and to create
less confusion) to have some "ASCII" equivalent so that it could be
maintained in 'text files' such as GenBank records?

Just a thought ... I'm pretty sure it would be difficult (and
probably:  not desirable) to convince the whole pombe community to
change the way they annotate their genes and gene products  ... but I
think you are painting yourself into a corner if you are not careful of
things like that!

I admit that my view of the world is jaded by the computer screen, and
that most people may be using printed text which has easier ways of
dealing with text formating, but I think that for a long time still
database records will continue to be the vehicle for information about
genetic databases, and that the ability to clearly 'depict' this
information in a text-based fashion will ensure that everybody will be
talking about the same thing.

comments?


francis

--
| B.F. Francis Ouellette  
| GenBank
|
| francis at ncbi.nlm.nih.gov   
  


>  
> Big difference #1:  No capitalization ever for genetic loci
> Big difference #2:  No difference for dom/recessive
> 
> you will sometimes see in the older literature the allele designation
> separated by a full stop (cdc2.33) instead of a hyphen (cdc2-33)
> Also, allele designations may be compound (ie, ade6-M210, cdc2-3w), 
> not simply numbers.
> 
> Protein designations are fluid;  the main difference is that they
> are not italicized, but people vary as to whether they use 
> capitalization or the appended p.  IMO, Cdc2p  is preferred but
> you will also see Cdc2, cdc2, and cdc2p. 
> 
> There is a note about nomenclature on our pombe methods web page
> (http://flosun.salk.edu/~forsburg/plasmids.html)
> 
> Hope this helps!
> 
> susan
> 
> ><><><><><><><><><><><><><><><><><><>
> S L Forsburg                             
> susan_forsburg at qm.salk.edu        
> http://flosun.salk.edu/~forsburg
>  "I don't speak for the Institute,         
>  and the Institute doesnt speak for me."
> 
> 



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