[Biopython] Code for protein alpha helix prediction

[Frank Kauff]

Hi Peter,

for the start, it seems psipred is the easiest one to use and to 
implement. I'll start with that, and once the parser for the output goes 
beyond the quick-and-dirty level, we can think about including it.

Frank

On 04/20/2010 05:43 PM, Peter wrote:
> On Tue, Apr 20, 2010 at 3:27 PM, Frank Kauff<fkauff at biologie.uni-kl.de>  wrote:
>    
>> Hi all,
>>
>> I've recently been asked to help with screening protein sequences for
>> certain features, something I don't really know much about... Yet!
>>
>> My questions: Is there some code in Biopython that allows for a quick check
>> whether an amino acid sequece is likely to be a alpha helix? Couldn't find
>> any. Or is there an algorithm that could be straightforwardly implemented in
>> python, or a commandline tool that could be called from within a python
>> script?
>>      
> Hi Frank,
>
> There are lots of tools for predicting secondary structure (alpha helices,
> beta sheets etc) both de novo, and guided by reference sequences with
> known structures. Some of these are online web services.
>
> I'm pretty sure there is nothing for this built into Biopython, so for scripting
> this for a large number of sequences then (as you have also suggested),
> my first approach would be to look for command line tools which you could
> call from Python. I've never needed to do this myself, and have no specific
> recommendations regarding which tools to try first.
>
> If you do find some useful algorithms which could easily be implemented
> in Python, they could be worth including - maybe under Bio.SeqUtils?
>
> Peter
>