Question: python dynamic output for biological sequences
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gravatar for andynkili
3 months ago by
andynkili10
andynkili10 wrote:

My goal is to output Coding DNA Sequences (CDSs) from different (but closely related) whole genomes sequences in a dynamic way.
I have a variable number of genome sequences and their related CDSs (with their names, positions, and also their differences (SNPs) for common CDSs across different genomes ).
I would like to draw the CDS per genomes on a single line as boxes (or arrows for reading frame issue ) with their names inside. So far i managed to do it using SeqFeature and Graphics from biopython (here is my result) but the output can only be saved in non-interactive format (jpeg, pdf, ...). The dynamic part of the output would allow to add further details on each CDS:

  • mousing over them would print more information (size, sequence in protein, SNPs)
  • clicking would allow to download the sequences

I don't have a clue on how produce an interactive output able to display those information. Could someone give some hints about achieving such results? Any python librairies? Any other tools?

genome draw python gene • 160 views
ADD COMMENTlink written 3 months ago by andynkili10

SVG graph may provides simple interaction.

ADD REPLYlink written 3 months ago by shenwei3563.4k

You could try using something like D3 which has python implementations to make interactive graphs etc. Here's an online guide.

A friend of mine wrote BRIG in java, and then a fan of the software who wanted interactive outputs reimplemented it via D3.

ADD REPLYlink written 3 months ago by jrj.healey3.0k

I think you can easily do this with R/shiny. See https://github.com/Bioconductor/CSAMA2015/tree/master/materials/lectures/1_Monday/L01-BAMSpector for a simple related example

ADD REPLYlink written 3 months ago by Asaf4.6k
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