Question: How to visualize gene structure of a (prokaryotic) locus?
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gravatar for ivan.antonov
7 months ago by
ivan.antonov70
Moscow, Russia
ivan.antonov70 wrote:

Hello, guys!

I was wondering, how an image like this can be automatically (programmatically) generated from the initial data in a text file?

enter image description here

The figure is taken from https://www.ncbi.nlm.nih.gov/pubmed/29168502

Could anyone recommend a good R package for this?

Thanks in advance, Ivan

python gene visualisation R genome • 560 views
ADD COMMENTlink modified 7 months ago by h.mon24k • written 7 months ago by ivan.antonov70

You can try EasyFig. It does pretty nice figures.

That looks similar to the output of MultiGeneBlast, but I’d wager it was probably made by hand.

ADD REPLYlink written 7 months ago by jrj.healey11k

Thanks for the response! It may be difficult to accurately visualize the gene lengths and intergenenic distances by hand, though..

ADD REPLYlink written 7 months ago by ivan.antonov70

what would be your input ? a GFF ? a genbank file ?

ADD REPLYlink written 7 months ago by Pierre Lindenbaum119k

Yeah, something like GFF format. I can prepare a list of genomic coordinates for the genes of interest in any format...

ADD REPLYlink modified 7 months ago • written 7 months ago by ivan.antonov70

Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

ADD REPLYlink written 7 months ago by h.mon24k

Thanks for the link!

ADD REPLYlink written 7 months ago by ivan.antonov70
4
gravatar for h.mon
7 months ago by
h.mon24k
Brazil
h.mon24k wrote:

I just found the gggenes R package, it seems it was designed with your question in mind. See a small example in my answer to Genome Diagram in R.

ADD COMMENTlink modified 7 months ago • written 7 months ago by h.mon24k

This is just perfect -- thanks a lot!

ADD REPLYlink written 7 months ago by ivan.antonov70
2
gravatar for jrj.healey
7 months ago by
jrj.healey11k
United Kingdom
jrj.healey11k wrote:

You might also be interested in the forum I threw together a while back.

Many of the tools in that thread will do what you need.

Interesting/useful/beautiful bio sequence viz tools

ADD COMMENTlink written 7 months ago by jrj.healey11k

Thanks -- DNAFeaturesViewer and GenomeDiagrams python libs look like what I need:)

ADD REPLYlink written 7 months ago by ivan.antonov70
2
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Use the XML genbank output of NCBI Eutilities for your genome and transform it using a XSLT stylesheet to SVG. Here is an example using two accessions in the range 1000-50000.

you can then edit it with inkscape.

ADD COMMENTlink written 7 months ago by Pierre Lindenbaum119k
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