looking for a free software for manual sequence annotation

Question

[m.rothierbautzer]

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!

[piet]

In general this involves two steps:

1. annotating a new sequence, results are typically stored in GFF or GB files
2. visualization of already annotated sequences

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.

Answer 1

[Andrzej Zielezinski]

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).

Answer 2

[Ibrahim Tanyalcin]

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,