Debian package for TeXtopo
The Debian-Med software list mentions textopo as a LaTeX extension to
display the topology of transmembrane proteins.
An ITP is still pending, otherwise the package is ready for an upload
to the main distribution from my point of view. Is anybody of you
familiar with Debian standards for TeX and would sponsor me? The package
is at
http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/textopo/
Cheers,
Steffen
>From http://homepages.uni-tuebingen.de/beitz/tte.html:
PHD topology predictions are a mighty tool to localize transmembrane
domains and the protruding loops. SwissProt database files provide
sequence feature informations, such as mutation sites, important
domains, or secondary modifications. Making these data visible in a
sophisticated topology plot is an enormous effort when using a standard
drawing software.
TeXtopo is a LaTeX2e macro package that provides two new environments:
(a) the 'textopo' environment is used for plotting topology data of
membrane proteins derived from PHD predictions, from SwissProt database
files or from manually entered data containing sequence and
transmembrane domain information, and (b) the 'helical wheel'
environment draws transmembrane domains as seen from above or beneath
the cell membrane.
Both kinds of plots can be richly decorated with special shading for
domains of interest, plus labels and legends. TeXtopo is fully
compatible with TeXshade (v1.3 and up) -- the comprehensive alignment
shading package for the TeX community. This allows one to apply
calculated shading based on sequence conservation and functional aspects
of the residue sidechains.
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