enhanced DNA sequence track

[rbuels]

Add options to show:

• [x] 6-frame translation with start and stop codons highlighted
• [ ] canonical splice sites
• [ ] GC content when zoomed out

[rbuels]

can probably adapt some of the 6-frame code from the webapollo sequence track.

[ghost]

I've checked webappolo. That seems a good solution. Thank you very much Robert. We are currently migrating to JBrowse on most of applications used internally and developed by our group . Besides that, we currently using JBrowse as RNA-Seq/Genotype viewer at AspGD, a collaboration between Broad and Stanford. See below a locus page containing the link to a Jbrowse instance: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN1226#summaryParagraph Thanks again. Best regards,

[BrianFoley]

Is it possible to display an amino acid track (or tracks) in one letter or three letter code, for the annotated genes in a GFF file? For example if I want to browse an annotated virus genome, or an annotated eykaryotic chromosome or contig, I would like to see the amino acids of the encoded proteins for the genes that are annotated in the file.

This feature, plus the view 6 frame translations with start/stop and slice sites highlighted, would be useful for scanning for potential genes that did not get annotated.

[rbuels]

That kind of functionality would probably best come from porting the GBrowse cds glyph to JBrowse. I opened issue #320 for that.

[selewis]

I think we need to take this opportunity to reflect and make sure that we think about the optimal solution rather than simply mimicking GBrowse in JBrowse.

-S

On Aug 16, 2013, at 12:01 PM, Robert Buels notifications@github.com wrote:

That kind of functionality would probably best come from porting the GBrowse cds glyph to JBrowse. I opened issue #320 for that.

— Reply to this email directly or view it on GitHub.

[jorvis]

The release notes for the 1.10.3 maintenance release suggest this has been completed and references this issue number. Should this be closed?

[rbuels]

@jorvis Still need to do the canonical splice sites, which is why it's still open.

[rbuels]

@kamalkumar said:

When zoomed out, the reference track shows a big gray area with the text "Zoom in to see sequence" repeated across the track. It would be nice if the reference track adapts to some meaningful display when zoomed out. If that is not possible, then dynamically hiding it would be better when zoom out level is large enough for it to not show the bases etc. (JBrowse version 1.10.8)

[scottcain]

Hmm, so this feature request has been open for kind of a long time :-)

Can I add to it, or should I go ahead and create a new issue for "further enhancements to the reference sequence track"?

[rbuels]

@scottcain I'd say add to it

[scottcain]

1. I would like to be able to color the backgrounds of the sequence track separately for forward and reverse strands. The reason this is a nice thing to do is to work nicely with the ColorByCDS plugin: when you're looking at a zoomed in view of a CDS and you can see the sequence track too, the ability to color all six frames would let the user know unambiguously which translation they should look at.
2. Related to this, I would like to be able to change the color of the backgrounds of the translations (all 6!) via callback or config options, which may be possible now, but it's not clear to me.

[rbuels]

[rbuels]