Question: How to visualize gene structure of a (prokaryotic) locus?
0
gravatar for ivan.antonov
8 weeks ago by
ivan.antonov50
Moscow, Russia
ivan.antonov50 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 • 371 views
ADD COMMENTlink modified 8 weeks ago by h.mon21k • written 8 weeks ago by ivan.antonov50

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 8 weeks ago by jrj.healey8.4k

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

ADD REPLYlink written 8 weeks ago by ivan.antonov50

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

ADD REPLYlink written 8 weeks ago by Pierre Lindenbaum114k

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ivan.antonov50

Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

ADD REPLYlink written 8 weeks ago by h.mon21k

Thanks for the link!

ADD REPLYlink written 8 weeks ago by ivan.antonov50
4
gravatar for h.mon
8 weeks ago by
h.mon21k
Brazil
h.mon21k 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 8 weeks ago • written 8 weeks ago by h.mon21k

This is just perfect -- thanks a lot!

ADD REPLYlink written 8 weeks ago by ivan.antonov50
2
gravatar for jrj.healey
8 weeks ago by
jrj.healey8.4k
United Kingdom
jrj.healey8.4k 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 8 weeks ago by jrj.healey8.4k

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

ADD REPLYlink written 8 weeks ago by ivan.antonov50
2
gravatar for Pierre Lindenbaum
8 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k 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 8 weeks ago by Pierre Lindenbaum114k
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