[Bioperl-l] Module to draw transmembrane protein topology
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/).
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.
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