[Biococoa-dev] BCNucleotideRNA

Koen van der Drift kvddrift at earthlink.net
Fri Sep 24 21:20:16 EDT 2004

-----Original Message-----
From: Alexander Griekspoor <mek at mekentosj.com>
Sent: Sep 24, 2004 1:46 AM
To: Koen van der Drift <kvddrift at earthlink.net>
Cc: John Timmer <jtimmer at bellatlantic.net>, 
	BioCocoa Mailinglist <biococoa-dev at bioinformatics.org>
Subject: Re: [Biococoa-dev] BCNucleotideRNA

> In that case, should all the occurances of 'base' in the code be 
> replaced by 'nucleotide'?
Officially yes. I'm in favour of that as well, but leave it up to you, 
as you have created these classes.

Actually, these are John's classes, so I'll leave it up to him.

> Eg in isSingleBase, representedBases, etc. It's up to you guys, 
> whatever you think is more accepted in the field.  Also, when we do 
> the MW calculation of a BCNucleotideDNA, we actually are calculating 
> just the MW of the bases? If so, should we add the mass of a 
> (deoxy)ribose and a phosphate to each unit?
We should definitely calculate nucleotide masses instead of those of 
bases, but I have no clue if we're doing that already....

I will check that this weekend, and make some changes, if needed.

- Koen.

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