[Biopython] Code for protein alpha helix prediction
Frank Kauff
fkauff at biologie.uni-kl.de
Wed Apr 21 11:59:31 UTC 2010
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
>
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