Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        Yesterday, 01:16 PM
      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 07:15 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 10:28 AM
      0 responses
      15 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 07:35 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-22-2024, 02:06 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Working...
      X