[Biopython-dev] PCR module

[Yair Benita]

on 27/5/02 11:16, Dmitri I GOULIAEV at dmitri.gouliaev at telkel.net wrote:

> Hi, Yair Benita !
> 
> On Mon, May 27, 2002 at 09:34:39AM +0200, Yair Benita wrote:
> 
>> I suggest 2 different modules: PCR module and Analysis module.
>> The Analysis module will handle everything related to DNA and Protein
>> sequence analysis.
>> The PCR module will use some methods from the analysis module (such as GC
>> content) and will have all methods relevant only to PCR (such as melting
>> temperature).
> 
> Wow ... This will be quite a module, if you will put EVERYTHING related to DNA
> and Protein SeqAn into it ...
> 
>> The PCR module will use some methods from the analysis module (such as GC
>> content) and will have all methods relevant only to PCR (such as melting
>> temperature).
> 
> It is not "relevant ONLY to PCR".
> 
> Probably, it is not such a bad idea to divide them like this:
> analysis
> `-- protein
>  `-- content
>  `-- surface
>  `-- hydrophobicity
>     `-- Kite-Doolittle
>     `-- Eisenberg
>  `-- secondary structure
>     `-- local
>     `-- global
> `-- nucleic
>  `-- melting temp
>  `-- GC content
> 
> What's about this: first level -- by object (protein or nucleic sequence),
> second level -- by what is obtained by this analysis.
> 
> It's just an idea, the list is not exhaustive.

In my module there are 2 classes: DNA and Protein.
The DNA class has access to the Protein class (upon translation of the DNA
sequence).
Each class has methods of analysis. Basically its not such a big module
because many analysis methods are just about listing/summing values of the
amino acids along the sequence. Its one method and a different file with all
the dictionaries for hydrophobicity, flexibility, MW,  etc.

I think we should exclude anything related to structure. If we want a module
for prediction of secondary structure then it should be a different one. The
analysis module will handle only primary structure analysis.

Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University