Question: Publication Quality, Cross-Platform, Alignment Visualization Tools
2
gravatar for jth
5.4 years ago by
jth190
Turkey
jth190 wrote:

Dear All,

I am looking for a software (free/open-source preferable) that can produce publication quality alignment images. An unfortunate requirement is that the software should be cross-platform as it will be used in a highly heterogeneous environment. Do you have any suggestions in this matter?

Thanks!

ADD COMMENTlink modified 5.4 years ago by Neilfws48k • written 5.4 years ago by jth190
1

Could you give an example of a publication quality alignment image? The ones I've seen differ _a lot_ in quality, and I suspect that in the nicer ones there's been some manual editing involved.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by David Westergaard1.4k

It sounds a lot like the job of IGV and Tablet, although the meaning of publication quality alignment image really depends...

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Sam2.2k

This is a slightly good instance i guess: http://www.nature.com/nature/journal/v392/n6671/images/392097ab.tif.2.gif It has been colored for particular reason in particular positions (it may be just to show sequence similarity, of course), It has well represented helices or other secondary structures, and it is easy to follow the alignment in the figure.

ADD REPLYlink written 5.4 years ago by jth190
1

That particular alignment actually looks like it's been done manually, especially since it's from a '98 article. Also, I believe the residues are coloured by physical properties. E.g. if all residues on the same position are non-polar. There's quite a few different kind of markups, each having its own merit.

If you want that kind of alignment, though, I think your best best if to look into IGV or Tablet, as someone mentioned. Another (free) option would be Jalview, however that doesn't add in secondary structure to the actual alignment, so you would have to do that yourself. And it's run in Java, so it's fit for a cross-platform environment.

ADD REPLYlink written 5.4 years ago by David Westergaard1.4k
0
gravatar for Neilfws
5.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You could start with Wikipedia's list of alignment visualization software. However, it is incomplete.

You could web-search for "multiple alignment secondary structure publication quality". Top hit is STRAP, which looks like it could do what you want.

I used to use Alscript for this purpose, back in the 1990s. It's still available and maintained.

ADD COMMENTlink written 5.4 years ago by Neilfws48k
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