Question: Low Resolution Sequence Alignment Visualization
1
gravatar for greenberg.charles.h
5.7 years ago by
greenberg.charles.h10 wrote:

I'm looking for a tool (or suggested code) on how to illustrate a multiple sequence alignment in a very coarse manner, so that it can fit in a small figure. The point isn't to show specific amino acids, just to show where there are large gaps in the alignment. Really it's inspired by this image:

Cool alignment

Any suggestions or pointers to code (eg matplotlib) would be greatly helpful. Thanks!

ADD COMMENTlink modified 5.7 years ago by Pierre Lindenbaum119k • written 5.7 years ago by greenberg.charles.h10
4
gravatar for Pierre Lindenbaum
5.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Ok, just for fun I reinvented the wheel (But I might use this code to display a BAM alignment in the future). I wrote a java program reading a clustal file and writing a SVG file (that you can later edit with inkscape): see https://github.com/lindenb/jvarkit#biostar77288

tested with: http://www.tcoffee.org/Courses/Exercises/saragosa_pb_2010/practicals/practical_2/ex.1.19/file/clustalw.msa

enter image description here

ADD COMMENTlink written 5.7 years ago by Pierre Lindenbaum119k

and Tim Yates wrote a groovy version: https://twitter.com/tim_yates/status/359990843546935297

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Pierre Lindenbaum119k
1
gravatar for Alex Reynolds
5.7 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

If you can convert your data into GFF3-formatted elements, GenomeTools offers gt sketch that might help you out. Render into PDF and you can do markup with Adobe Illustrator or Inkscape.

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Alex Reynolds28k
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