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

Jeffrey Chang jchang at smi.stanford.edu
Fri May 24 05:10:45 EDT 2002

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.


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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