[Biopython-dev] PCR module

[Dmitri I GOULIAEV]

Hi, Yair Benita !

 On Mon, May 27, 2002 at 11:38:29AM +0200, Yair Benita wrote:

> 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).

I would add the folder ``mixed'' to my hierarchy:

seq analysis
`-- protein
    . . .
`-- nucleic
    . . .
`-- mixed
   `-- translation
   `-- ORF search

etc.

> 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. 

Sure, I agree with you.

> The analysis module will handle only primary structure analysis.

Ah, OK !
Because, at the first glance to your proposition I saw all the analysis put in one module. 

I don't think we should make a separation into the modules by complexity of algorithm used. In my opinion, the functionality would be more suitable for this.

Best regards,

-- 
DIG (Dmitri I GOULIAEV)

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