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Library For Perl Protein Sequence Visualisation

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?

visualization protein
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updated by Neilfws Neilfws • written by Niallhaslam Niallhaslam

3 answers

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/

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Like the idea of using SVG as the final output.

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written by Niallhaslam Niallhaslam

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?

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written by dimkal dimkal

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

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written by Niallhaslam Niallhaslam

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

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written by Neilfws Neilfws

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

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written by Niallhaslam Niallhaslam

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