I want to make a figure which have a sequence and its structure Annotated on top of it. If somebody knows any software related to this then please let me know. I am not asking any structure prediction or sequence alignment tool.
There is also Alscript, which can be difficult to use at first as there is no gui just scripting but can be powerful and gives you a lot of control. It allows you to edit your sequence alignment easily with annotations etc. (http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html)
There is also Strap which has a gui and is also useful. (http://www.bioinformatics.org/strap/index2.html)
Hi,
I usually use Espript for this kind of figures (http://espript.ibcp.fr/ESPript/ESPript/ ). It is not to difficult to handle for simple figures, and once you get used to it, you can generated quite complicated sequence alignments...
You can also try PROMALS3D multiple sequence and structure alignment server.
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