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Tool For Plotting Protein Architecture/Domains

I am looking for a tool that can plot a protein domain graph (similar to how it is done in Pfam or Smart) from an input file containing domain coordinates and protein size. By searching the web, I found two tools that almost fit the bill:

  • DOG (http://dog.biocuckoo.org) creates nice figures, but is geared to interactive usage. I did not find a way how to run this program in batch mode, e.g. by reading the domain coordinates from a file.
  • MyDomains (http://prosite.expasy.org/mydomains) is closer to what I need. It is primarily a web server, but it offers to d batch runs by stuffing all domain coordinates into a stable URL that returns a bitmap figure.

Is anybody aware of a similar tool that supports batch mode, does not require me to learn a new programming language, and is powerful enough to generate nice figures. Ideally, it would support to put multiple proteins into one figure.

Thanks a lot!

domain visualization protein protein-structure
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updated by Michael Dondrup Michael Dondrup • written by Lyco Lyco

You can try ggplot R package using script (simple commands) to combine all the coordinates in one file and then plot in one shot.

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written by H@rry • H@rry

I was actually looking for something similar scriptable for multiple proteins but could not find anything satisfactory. So I wrote a program in python which can give output in svg/pdf/png and has all possibilities like svg. I am wondering if I can actually write a small paper and put it as a web service since lot of people are looking for something like this.

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written by Pappu Pappu

yeah could be. It would be nice idea. Good luck

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written by H@rry • H@rry

1 answer

You can try mkdom/xdom tools with ProDom suite at http://prodom.prabi.fr/prodom/current/html/home.php . These tools can be freely downloaded after signing License at http://prodom.prabi.fr/prodom/current/html/download.php .

• 196 views • link
updated by Khader Shameer Khader Shameer • written by himanshu17 • himanshu17

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