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From: Ron June on 19 Jul 2010 19:58
Hi All,

I'm new to bioinformatics with MATLAB, and my web and documentation searches have thus far not helps, but I apologize for potentially not knowing what to search for.

Anyway, I'm analyzing the primary amino acid sequences of ~500 proteins, and I'd like to be able to work with some of the data generated by the proteinpropertyplot function (eg find the zero-crossings for a hydrophobicity plot.)

Does anyone know code to export the data to the workspace?

Thanks!
From: Lucio Cetto on 20 Jul 2010 06:39
Ron:
The PROTEINPLOT GUI has an "Export to workspace" tool. You can use it for one or two of your sequences. If you want to programmatically repeat the process for all your sequences I recommend to use PROTEINPROPPLOT function with one output argument, here is an example to find zero crossings:

prion = getpdb('1HJM', 'SEQUENCEONLY', true)
data = proteinpropplot(prion,'property','hydrophobicity (Kyte & Doolittle)')
zero_crossings_indices = data.Indices(diff(sign(data.Data))~=0)
plot(data.Indices,data.Data,'-')
hold on
plot(zero_crossings_indices,0,'ro')

HTH
Lucio

"Ron June" <rkjune(a)gmail.com> wrote in message <i22oqc$fgg$1(a)fred.mathworks.com>...
> Hi All,
>
> I'm new to bioinformatics with MATLAB, and my web and documentation searches have thus far not helps, but I apologize for potentially not knowing what to search for.
>
> Anyway, I'm analyzing the primary amino acid sequences of ~500 proteins, and I'd like to be able to work with some of the data generated by the proteinpropertyplot function (eg find the zero-crossings for a hydrophobicity plot.)
>
> Does anyone know code to export the data to the workspace?
>
> Thanks!
From: Ron June on 20 Jul 2010 19:38
Works perfectly--thanks!
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