a BioC/R package that display the genome sequence/ mRNA exons/protein domains
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Bogdan ▴ 670
@bogdan-2367
Last seen 4 months ago
Palo Alto, CA, USA

Dear all,

would you please advise -- which BioC/R package shall i use in order to display on the same figure :

a-- the genomic sequence

b-- the coordinates of introns / exons

c-- the positions of the protein domains that the exons code for

d-- any other custom annotations related to DNA/ RNA /protein sequence

thanks a lot,

-- bogdan

AnnotationHubData • 586 views
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Kevin Blighe ★ 3.9k
@kevin
Last seen 5 weeks ago
Republic of Ireland

Hello my friend Bogdan,

With a combination of Gviz, GenomicRanges. and rtracklayer, you should be able to develop figures like this, if that is what you need:

h

This is from my own work from 2018.

As an alternative, you could also try Bernat's karyoploteR package: https://bernatgel.github.io/karyoploter_tutorial/

Kevin

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