[Biopython-dev] PCR module

[Thomas Sicheritz-Ponten]

Yair Benita <Y.Benita at pharm.uu.nl> writes:

> Thomas,
> I have looked at your sequtils module and I can add some code from my own
> PCR module:
> 
> Melting temperature of primers.
> Matching primers to a template, including primers with overhangs.
> Checking the frame of the product vs the template (only for primers which
> contain a gateway adapter, otherwise I cannot know the frame of the primer).
> 
> I plan to add some primer selection code but I first have to analyze 1600
> PCR reactions we did and improve the primer selection based on that.
> 
> Would you like to see the code and add it to your module or would you prefer
> that I write a module that uses sequtils and adds new methods?
> 
I am still moving from the danish university to the swedish university, so
I was not involved in any biopython discussions for a time ...

Anyway, the purpose of sequtils was more like a temporary storage module for
commonly used sequence analyzing utilities/functions. I hoped that most of
the functions would eventually find their way into the modules they
actually should belong too .... 

Whats the overall opinion of sequtils.py? 
* Should we reorganize the code and move "movable" functions before
  merging/adding PCR modules and documentation?
* Should we use it as it is (maybe after some cosmetic changes) and continue
  adding sequence analyzing methods?
* Or, should we split it into core sequence utilities (like GC content and
  sequence editing) and more user level defined sequence utilities (like 6
  frame translations, gc skews, graphical GC content etc.) (inherited from
  the core module)

Personally, I'd prefer the latter ... in this case we could have a PCR
module and avoiding duplicated code by putting common functions in the core
sequence utilities module (e.g. GC content, frames etc.)

Suggestions, ideas, critics???

its-hot-even-here-in-sweden'ly y'rs
-thomas

-- 
Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org      (
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