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I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence on top and tracks at the bottom that highlight which part is an alpha helix or a beta sheet.

My final annotated sequence would look like this:

What I want my annotated sequence to look like

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  • $\begingroup$ Benchling is free for academics and makes sequence annotation really easy. Check out an example sequence I annotated here: benchling.com/s/1m8QllV2/edit It's all on the web, so you can sign up at benchling.com :) $\endgroup$ – vpontis Dec 24 '15 at 16:47
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You might find some success with using WebApollo or JBrowse

WebApollo allows you to perform many manual annotation functions for your genes, such as editing exon boundaries, fixing coding sequences, and merging or splitting gene predictions, which looks like what might have been done in the UCA-At2g42245. It can also be used for adding various attributes, GO terms, pubmed info, or generic attributes. WebApollo actually uses JBrowse, but JBrowse itself has very flexible options for displaying annotations. The part about highlighting the alpha helix/beta sheets is not built in, but JBrowse can be configured to do lots of different renderings, and I could provide more details if you are interested. Disclaimer: I'm a WebApollo developer/JBrowse contributor.

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