This is for those who are interested in plotting microbial genomes in circular plots. You can easily plot classification-type data or numerical data (microarrays, proteomics or other computational data) in the program GenomeViz. Here is the manuscript. GenomeViz is free for academic users. Any comments are most welcome.
GenomeViz
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Nice work
Every few months, I comb the web for software to do this job. We have discussed a few packages here before - GenomeDiagram (Python) and something called psu_diagram (Perl), which is buried so deep in the Sanger Centre FTP site that I can't find it right now. I also have an aged Tk app called Genomap, from a Japanese group.
Anyway, your effort looks superior to all of these - well done.
GenomeViz - Rohit
Thank you Neil. I'll soon be adding a few more (hopefully) useful features. In case you have any features you'd like to have please feel free to suggest them.
Problems...solutions?
My initial enthusiasm has cooled a little once I tried to install the package. First, it complained that my Debain system was missing some Tk widgets - this was easily fixed with "apt-get install iwidgets4". Now, "./GenomeViz.tcl" gives me:
X Error of failed request: BadValue (integer parameter out of range for operation)
Major opcode of failed request: 45 (X_OpenFont)
Value in failed request: 0x2e00006
Serial number of failed request: 36
Current serial number in output stream: 37
Suggestions?
GenomeViz
As promised, here is a new version of GenomeViz. It included some useful features and new plotting options for quantitative data. Do get in touch if you face installation problems. Once again, please try the installation as in the manual and use ActiveTcl from ActiveState.
project home page:
http://www.uniklinikum-giessen.de/genome/genomeviz/intro.html
Works this time and looks good
I have downloaded and installed (with the addition of iwidgets4 on Debian - Debian has plenty of Tcl/Tk packages and I didn't want to mess up my libraries with ActiveState).
This time, works great and looks very nice.
GenomeViz
Fantastic! , I don't think you would get a problem with your
other libraries
You could install ActiveTcl anywhere and modify the third line in GenomeViz script (without messing with your PATH variable)
original line:
exec wish "$0" ${1+"$@"}
modified line:
exec /home/someuser/ActiveTcl/bin/wish "$0" ${1+"$@"}
GenomeViz installation solution.
I have not tested GenomeViz on Debian. And you should not have needed to install the Iwidgets package separately. Maybe you should just try and install ActiveTcl from ActiveState rather than installing Iwidgets separately. Let me know (by email) if there are problems after that. You can reach me from the GenomeViz home page
http://www.uniklinikum-giessen.de/genome/genomeviz/intro.html
Rohit
Genome visualization is alway
Genome visualization is always good. The previous discussion of GenomeDiagram is here. The link for that Perl program from the Sanger center is also there.
Everyone in Taiwan will be celebrating Chinese new year next week so hopefully I'll find some time to finally upgrade the nodalpoint cms. This should bring back search so we can find previous discussions like this one.
Also I had to reformat the post due to a formatting bug in the CMS (adding erroneous line breaks in links) that crops up from time to time.