[Bioperl-l] Module to draw transmembrane protein topology

Chris Fields cjfields at uiuc.edu
Tue Feb 20 11:09:00 EST 2007


On Feb 20, 2007, at 9:50 AM, Tim Nugent wrote:

> Labeling of inside/outside and membrane is already possible via - 
> inside_label, -outside_label and -membrane_label tags, defaults are  
> intracellular, extracellular and plasma membrane.
>
> Was definitely going to add an input/parser for MEMSAT, developed  
> here at UCL, and probably a few other popular TM predictors too,  
> e.g. PHOBIUS, TMHMM etc. Can already accept topology in the string  
> format used by OPM (http://opm.phar.umich.edu/).
>
> Tim

I'll definitely have to take a closer look at it when I have time.   
My guess is the best fit for data would be a seqfeatures, either in a  
collection or a Bio::Seq.  As for the parsers you can look at the  
Bio::Tools::Tmhmm module, which scans Tmhmm output and converts  
everything to seqfeatures.

chris


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