[Biococoa-dev] BCNucleotideRNA

[Alexander Griekspoor]

> Does anyone
> have a preference for prioritizing these sorts of situations?  Careful
> coding with build failure vs. a bit more sloppy with things always 
> working?

I would say the first, BUT that would be if I was alone because then I 
know exactly what is the problem and what I still have to do to make it 
work again. Here we are with more people and the problem is that if two 
people are in this situation, you start fixing things and still it 
doesn't work. Second, if I as a third person would like to do a lot of 
testing, I can't because the framework doesn't build. Thus, I guess we 
should only check things back in if it works again, until then just 
keep things for yourself until you're finished, or have something that 
works. Careful coding with things always working ;-)
>
>> uridine  (uri·dine) ([umacr]r¢[ibreve]-d[emacr]n)  a pyrimidine
>> nucleoside, uracil linked by its N1 nitrogen to the C1 carbon of
>> ribose. It is a component of ribonucleic acid, and its nucleotides
>> participate in the biosynthesis of polysaccharides and some
>> polysaccharide-containing compounds. Symbol U.
>>
>> So is it uridine or uracil ? I think uracil as we're talking about the
>> complete nucleotide right, not only the base...
>> That would be my daily portion of nitpicking ;-)
> Actually, your decision is right, but you misread the definition.  
> Uridine
> == uracil + sugar.  I tried to keep that consistent for all bases.

You're right, I see it now. These are the typical things I had to learn 
once, but forgot again ;-)

A nucleoside (with an s) consists of a nitrogenous base covalently 
attached
to a (ribose or deoxyribose) sugar but without the phosphate group.

A nucleotide (with a t) consists of a nitrogenous base, a sugar, and a
phosphate group. So, a nucleotide is a "nucleoside mono-phosphate."

A nucleic acid contains a chain of nucleotides covalently linked 
together to
form a sugar-phosphate backbone with protruding nitrogenous bases. In 
RNA
(ribonucleic acid), the sugar groups are ribose, whereas in DNA
(deoxyribonucleic acid), deoxyribose sugars are present instead of 
ribose.

So uracil is the base, uridine is the nucleotide. It's funny to see 
that (like me) almost everyone mixes these things up. Much like 
homologous and orthologous...


> An unrelated aside:  does anyone know of an example of an ObjC class 
> with
> detailed comments where headerdoc can do its magic properly?  I'd love 
> to
> find out what I'm doing wrong there, but can't figure out how to 
> google for
> such a beast....

http://sourceforge.net/projects/agkit/
I had the example from AGRegex part of the AGKit you can download from 
the link above. I'm not sure if that one is 100% correct though...

Cheers,
Alex


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                     ** Alexander Griekspoor **
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              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
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                    Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

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