Hello!
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.
it would look like this:
Thank you!
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written
by
m.rothierbautzer •
2 answers
For automatic annotation of genomic sequence I recommend the Maker program (if you work on plants use MakerP)
MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. As a result, MAKER returns a single GFF3 file containing the evidence from various gene prediction steps. This file can then be loaded in Apollo or Artemis. These programs are a way better for annotating genes than JalView (you can edit, drag-n-drop your gene models).
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written
by
Andrzej Zielezinski
Hi rothierbautzer,
I guess you are working with sequences that actually code for a protein.In that case you can use I-PV at http://i-pv.org/. If you want to plot secondary structure, you can do it as shown here: http://i-pv.org/intro_ipv_alt3.html
You can mark the exons/domains using the connectogram or coloring.
For tutorial of generating such graphs see here: http://i-pv.org/intro_ipv_alt4.html
I hope this helps,
Good luck,
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written
by
Ibrahim Tanyalcin
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In general this involves two steps:
Each step requires very different software. Choice of software for the annotation step also depends much on the organism you are working on. Please clarify, what you are looking for.