Library For Perl Protein Sequence Visualisation

Question

[Niallhaslam]

Hi all,

I'm looking for a library to draw, annotate and visualise protein sequences, ideally in Perl. Aside from the Tcl/tk library what else is out there. Does anyone use the GD library and would they recommend it?

Alternatively, assuming the data is in an accessible format what other libraries, toolkits would people recommend?

Answer 1

[Pierre Lindenbaum]

it depends what's your original input and what you want to get at the end. For example, you could use a Genbank/XML file from the NCBI, transform it to SVG using XSLT (for example that one:

https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl)

and edit the resulting SVG file with http://inkscape.org/

[Niallhaslam]

Like the idea of using SVG as the final output.

Answer 2

[dimkal]

I usually use Jalview (http://www.jalview.org/examples/examples.html) for all my sequence visualization/annotation. can you provide an example of what you'd like to do?

[Niallhaslam]

Hadn't thought of using Jalview. Is it scriptable?

Answer 3

[Neilfws]

Bio::Graphics is the obvious choice. Start with the HOW-TO (not specific to protein sequence but same principles apply).

[Niallhaslam]

Thanks - that's the kind of thing I'm after for this project.