Question: How to visualize gene structure of a (prokaryotic) locus?
0
gravatar for ivan.antonov
9 days 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 • 279 views
ADD COMMENTlink modified 7 days ago by h.mon19k • written 9 days 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 9 days ago by jrj.healey6.8k

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

ADD REPLYlink written 9 days ago by ivan.antonov50

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

ADD REPLYlink written 9 days ago by Pierre Lindenbaum112k

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

ADD REPLYlink modified 9 days ago • written 9 days ago by ivan.antonov50

Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

ADD REPLYlink written 9 days ago by h.mon19k

Thanks for the link!

ADD REPLYlink written 9 days ago by ivan.antonov50
4
gravatar for h.mon
7 days ago by
h.mon19k
Brazil
h.mon19k 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 days ago • written 7 days ago by h.mon19k

This is just perfect -- thanks a lot!

ADD REPLYlink written 7 days ago by ivan.antonov50
2
gravatar for jrj.healey
9 days ago by
jrj.healey6.8k
United Kingdom
jrj.healey6.8k 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 9 days ago by jrj.healey6.8k

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

ADD REPLYlink written 9 days ago by ivan.antonov50
2
gravatar for Pierre Lindenbaum
9 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k 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 9 days ago by Pierre Lindenbaum112k
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