[Biopython-dev] New module for analysis of DNA and Protein sequences

[Yair Benita]

I see that some are duplicates. I was not aware of these functions. Thomas
wrote it for PCR related issues. I have other things in mind. Maybe I can
fix it to use the code of Thomas for the duplicated functions.

I also think we should seriously consider revising the documentation of
biopython. Many things have changed and if someone wants to know what kind
of methods are available in biopython he has to go though the code and read
the comments.

Regarding legal issues, I do not see any problems.
Is there a web page with instructions or guidelines? I could not find
anything on the biopython web site.

Yair

on 24/5/02 11:10, Jeffrey Chang at jchang at smi.stanford.edu wrote:

> Are some of these functions duplicates of existing biopython
> functionality?  I believe Thomas has already implemented some of this
> stuff in sequtils.py, so please work with him on figuring out how to
> integrate things.  I want to avoid duplicate code.
> 
> Also, be sure that you are willing to license it with the Biopython
> license, are willing to maintain it, and are the copyright holder and
> have the legal right to submit the code under these terms.
> 
> Jeff
> 
> 
> On Thu, May 23, 2002 at 01:21:26PM +0200, Yair Benita wrote:
>> Hi all,
>> I am doing some DNA and protein analysis and I have arranged all my scripts
>> in one module. It contains two classes: DnaAnalysis and ProteinAnalysis.
>> Both classes use a sequence object as input (from Seq.py).
>> 
>> DnaAnalysis: calculates nucleotide content, GC content,codon adaptation
>> index, translation to protein (with Tools.translate) and gives access to the
>> ProteinAnalysis class.
>> 
>> ProteinAnalysis: calculates amino acid content, molecular weight, protein
>> stability, flexibility, hydrophobicity, pi.
>> 
>> I also have a module for calculating the area under the curve. It is useful,
>> for instance, to know which fraction of a protein is hydrophobic and which
>> is hydrophilic. It is more informative than averaging. I am not sure if I
>> should include this.
>> 
>> Let me know what to do next. I am not sure how it works for submitting
>> modules and what is the procedure. Is someone checking the code?
>> 
>> Yair
>> -- 
>> Yair Benita
>> Pharmaceutical Proteomics
>> Utrecht University
>> 
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