[Biopython] Adding SVM in biopython

[Peter Cock]

On Tue, Feb 11, 2014 at 8:32 AM, Vishnu Chilakamarri
<vishnuc11j93 at gmail.com> wrote:
> Hello,
>
> I am currently working in a project to predict the GTP binding sites given
> an amino acid sequence. The classification algorithm I'm using is SVM. As
> of now I'm using SVM-light and python's scikit library for classification
> and evaluating the model.

Hello Vishnu,

General machine learning contributions would probably fit better
under the scikit libraries than in Biopython - their use goes way
beyond just biology after all ;)

> For adding this in biopython we can use libSVM as
> it has a python interface which can be used for this purpose.I would like
> to discuss the feasibility of adding this in biopython's library ...

Given libSVM has a Python interface, what would you be adding?
https://github.com/cjlin1/libsvm/tree/master/python

> and also evaluation metrics such as F1 score and MCC.
>

Isn't this already in scikit-learn?
http://scikit-learn.org/stable/modules/model_evaluation.html

Maybe I've not understood what you are suggesting?

Regards,

Peter