Print Alignment To Poster Format

Question

[Whetting]

Hi Biostars,
I would like to print an alignment of 241 sequences (~10,000 bp in length). I would likely print them on poster format (we have our own plotter). I am just worried about resolution. Does anyone know of an alignment editor that saves the alignment in some kind of scalable format? thanks

[Damian Kao]

You can probably just copy the alignment text and save it as a pdf. Why are you printing out this alignment? Perhaps just highlighting domains or regions on your 241 sequences would be more informative than a huge alignment.

[Whetting]

I agree, it would be more informative to print domains, but I just think it would be really cool to see it, stare at it, you know almost like the matrix :)

[Neilfws]

Almost identical question: http://www.biostars.org/post/show/18793/protein-alignment-tool-with-vector-graphics-output/

Answer 1

[Andrzej Zielezinski]

Use Jalview, a multiple sequence alignment editor. The alignment view can be exported as a document, bitmap or vector image via the File→Export menu:

• HTML - for viewing in a web browser. Then, you can save an alignment view as the PDF file (File → Print → Save as PDF in all modern browser)
• PNG - a Portable Networks Graphics image
• EPS - an Encapsulated Postscript Document

The EPS file generated by Jalview or the PDF file created by your web browser contains vector graphics which are directly editable in graphics applications such as Adobe Illustrator or Inkscape. It means you can rescale your alignment image without loss of clarity.

Answer 2

[Zev.Kronenberg]

LaTeX is awesome. I use TexShade all the time for this purpose.

I think there are some online tools so you don't have to code in LaTeX.

http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/pdf/texshade.pdf

Edit:: yup you can Tex via biology workbench:

http://molbiol-tools.ca/Alignments.htm