[Biopython-dev] PCR module

[Jeffrey Chang]

On Mon, May 27, 2002 at 05:35:07AM -0500, Dmitri I GOULIAEV wrote:
> I would add the folder ``mixed'' to my hierarchy:
> 
> seq analysis
> `-- protein
>     . . .
> `-- nucleic
>     . . .
> `-- mixed
>    `-- translation
>    `-- ORF search

This looks reasonable.  Thomas (?), go ahead and create a new
directory called Bio/SeqAnalysis or Bio/SeqUtils to hold this code.  I
believe the bioperl equivalent is called SeqUtils.  I would prefer not
calling it Analysis; it seems too general, especially since we've
agreed that this package will not include structure analysis code!

Also, when you're integrating code, don't forget to include
Bio.Tools.Translate and Bio.Tools.Transcribe modules.  Those probably
belong in here as well.

> 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.

Agreed.

Jeff