Fwd: [Biococoa-dev] more ramblings

[Alexander Griekspoor]

Again! Man I got to remember to send my emails to the list as well....

Begin doorgestuurd bericht:

Van: Alexander Griekspoor <mek at mekentosj.com>
Datum: 18 november 2004 21:32:44 GMT+01:00
Aan: John Timmer <jtimmer at bellatlantic.net>
Onderwerp: Antw.: [Biococoa-dev] more ramblings

>  Anyway, to stir up more controversy around here, I had always 
> envisioned something along the following structure:
>
>  Sequence bundle
>  (groups related sequences)
>      |
>  Sequence wrapper
>  (holds features, notes, etc.)
>      |
>  Sequence
>

Yes, my idea exactly! Imagine a multi-fasta file, wouldn't it be 
fantastic to initialize such a sequence bundle directly from it? Or 
write one out to disk in fasta format.... Also, alignments could be a 
perfect subclass of a sequence bundle object (one that only in addition 
has to store the interrelated positions... Awesome!

>  The reason being that I see features as being abstractions, not 
> inherent to any type of sequence.
Yep, absolutely agree. We have feared to approach this problem a bit in 
the past, but this should be the underlying idea to keep in mind.

>  They’re mostly a bit of information and a range it’s relevant to. 
>  There are some exceptions to this – for example, a phosphorylation 
> site changes the MW of a protein – but they are largely exceptions.
I see some discussions already on the horizons rapidly popping up (you 
should have stopped with the previous sentence when everything was 
still perfect ;-)

>  These exceptions are going to be difficult to handle regardless – how 
> to tell if a site is or isn’t glycosylated is going to be very context 
> dependent.  The majority of features (ORFs, kinase domains, 
> restriction sites, etc.) don’t require that sort of heavy lifting.
I guess, I'm gonna read some emails in which we discussed this 
previously, we have been talking about this.


Alex
*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                    Fax:  + 31 20 - 512 2029
                    AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

       Microsoft is not the answer,
       Microsoft is the question,
       NO is the answer

*********************************************************

*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                    Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

	Claiming that the Macintosh is inferior to Windows
	because most people use Windows, is like saying
	that all other restaurants serve food that is
	inferior to McDonalds

*********************************************************
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