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  • Best visualization APIs for conserved gene clusters

    Hello!

    I have a couple of lists of neighboring genes from several genomes. The data reflect conserved neighborhoods, however, not all genes are conserved. I would like to display the single gene clusters in an overview picture (without the need of automatically mapping corresponding genes to each other). It is just about visualizing the genome names and the genes as arrows. But the whole process should support automation!

    One additional requirement considering the output format is that I still need to modify the coloring after the image has been rendered. Also, it should be possible to attach labels to the genes (= free text) as post processing. Some vector format should be fine.

    Each gene comes with its coordinates and its direction (+/-). I don't need homology search.

    I would like to automate the generation of images that visualize the conserved neighborhoods.



    The result should look like this:

    Genome 1 ----------|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ----------

    Genome 2 -----|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ---------------

    Genome 3 ----------|||||||||||||||| >---||||||||||| > -------------------- < ||||||||||||||| ----------

    ...

    ...

    Genome N ----------|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ----------




    Of course, I could start programming this myself, but it would be nice if it already exists as freeware.

    Can anyone help me? Best regards Sebastian

  • #2
    Are you envisioning cross-links between the co-linear regions? Kind of like this using Python, Biopython (GenomeDiagram) and ReportLab (for PDF/SVG/etc output)?
    In which I take a short diversion into colour theory, and share some code to automate colour selection for class data.



    Note this isn't a point and click GUI solution - rather it is a Python scripting approach.

    Comment


    • #3
      Thank you! Do you know if something similar exists for Java?

      Comment

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