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CroBiAd / DAWN

Diversity Among Wheat geNomes (DAWN)
http://crobiad.agwine.adelaide.edu.au/dawn/
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Full cds sequence #3

Closed jcsanchez2 closed 6 years ago

jcsanchez2 commented 6 years ago

Would be good to be able to retrieve the full cds and/or the amino acid sequence for a specific gene

nathanhaigh commented 6 years ago

Apparent the plugin FeatureSequence provides this functionality: https://github.com/tsaari88/FeatureSequence

Howevery, it hasn't been updated in an year or so and may not work with the new plugin system. Will need to test.

nathanhaigh commented 6 years ago

I have added this plugin and modified it slightly to skip exon features. This is because the plugin falls back to some old/slow rendering code for features which overlap. Our GFF3 files will contain cds and five_prime_UTR and three_prime_UTR features which overlap with exons. Since we cds + five_prime_UTR + three_prime_UTR = exons, we can circumvent the feature overlap detection and dynamic UTR definition code entirely.

  1. Right click gene model and select the "retrieve sequence" menu option: image

  2. Select your required transcript: image

  3. Highlight, choose letter case or ahow/hide the transcript subfeatures together with upstream/downstream flanking sequence: image

  4. Copy and paste the sequence from the window to wherever you need it.