Low Resolution Sequence Alignment Visualization

Question

[greenberg.charles.h]

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:

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

Answer 1

[Pierre Lindenbaum]

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

[Pierre Lindenbaum]

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

Answer 2

[Alex Reynolds]

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.