[BioPython] Creating a graphical interface to database of gene coordinates

[Peter (BioPython)]

Srinivas Iyyer wrote:
> Dear group, 
>  I am happy that I am slowly finding pyhonian projects
> related to my research area. 
> 
> Problem:
> 1. I have a database of human gene coordinates on
> chromosomes.
> 2. I have gene expression data from my lab concerning
> the genes I mentioned above. 
> 
> 3. I want to visualize expression data laid on
> chromosomes.

You may be able to produce chromosome diagrams with Leighton Pritchard 
and Jennifer White's program genomediagram:

http://bioinf.scri.sari.ac.uk/lp/programs.html#genomediagram

It will do both circular genomes diagrams (nice for bacteria) and linear 
ones - which would make sense for chromosomes.  I think I've seen 
examples with expression data shown in this way... certainly it could be 
done.

Note that this can produce PDF or bitmap output - but its not 
interactive.  There is also a GUI to go with it, but I have not looked 
at this.

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One final suggestion, is to consider looking at R/BioConductor - its a 
completely different language but I have seen examples where expression 
data is visualised on chromosomes.

http://www.r-project.org/
http://www.bioconductor.org/

You can even call R from Python, for example using RPy (R from Python),:

http://rpy.sourceforge.net/index.html

See also RSPython, an R/SPlus - Python Interface which I have not used 
personally:

http://www.omegahat.org/RSPython/

Peter