Question: Protein Alignment Tool With Vector Graphics Output?
1
gravatar for Dr.Bunsen
7.0 years ago by
Dr.Bunsen140
Dr.Bunsen140 wrote:

I'm making several figures that contain protein alignments. What are the best tools to use for creating protein alignments that are capable of outputting vector graphics? Ideally, I would like to use MUSCLE for the alignment. I would like to generate alignments and export them as vector graphics. Thanks.

alignment sequence multiple • 6.7k views
ADD COMMENTlink modified 2.8 years ago by Suzanne50 • written 7.0 years ago by Dr.Bunsen140

are you looking to do sequence or structural alignment?

ADD REPLYlink written 7.0 years ago by dimkal730

I'm only concerned with sequence.

ADD REPLYlink written 7.0 years ago by Dr.Bunsen140
4
gravatar for dimkal
7.0 years ago by
dimkal730
United States
dimkal730 wrote:

In case of sequence alignment, I'd recomment trying out Jalview. There you can save alignments as SVG and EPS files, to and then edit them with either Adobe Illustrator or Inkscape. Good luck.

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by dimkal730

Thanks, this turned out to be a very good solution.

ADD REPLYlink written 7.0 years ago by Dr.Bunsen140
4
gravatar for Dan Gaston
7.0 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

I came across this web-server: http://wavis.img.cas.cz that will take multiple sequence alignments in several different formats (including fasta) and output to several different graphical formats (including SVG). Click on Scheme Drawing on the sidebar to get to the input page.

You can use any alignment program you wish, as the actual alignment and visualization are separate tasks.

ADD COMMENTlink written 7.0 years ago by Dan Gaston7.1k
3
gravatar for Manu Prestat
7.0 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

You can use Seaview to run Muscle and edit your MSA as well. The "prepare PDF" functionality exports the result in a vectorial way.

ADD COMMENTlink written 7.0 years ago by Manu Prestat3.9k
0
gravatar for Suzanne
2.8 years ago by
Suzanne50
Dundee, Scotland
Suzanne50 wrote:

I would recommend using Jalview (www.jalview.org), it can run the MUSCLE MSA algorithm, then allow you to customize the MSA viewer and export SVG figures. I have added links to YouTube videos about Jalview and how to customise and export figures.

ADD COMMENTlink written 2.8 years ago by Suzanne50
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