How to visualize gene structure of a (prokaryotic) locus?

Question: How to visualize gene structure of a (prokaryotic) locus?

16 months ago by

Moscow, Russia

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 • 873 views

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modified 16 months ago by h.mon ♦ 29k • written 16 months ago by ivan.antonov • 80

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 REPLY • link written 16 months ago by Joe ♦ 16k

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

ADD REPLY • link written 16 months ago by ivan.antonov • 80

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

ADD REPLY • link written 16 months ago by Pierre Lindenbaum ♦ 125k

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

ADD REPLY • link modified 16 months ago • written 16 months ago by ivan.antonov • 80

Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

ADD REPLY • link written 16 months ago by h.mon ♦ 29k

Thanks for the link!

ADD REPLY • link written 16 months ago by ivan.antonov • 80

16 months ago by

h.mon ♦ 29k

Brazil

h.mon ♦ 29k 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 COMMENT • link modified 16 months ago • written 16 months ago by h.mon ♦ 29k

This is just perfect -- thanks a lot!

ADD REPLY • link written 16 months ago by ivan.antonov • 80

16 months ago by

Joe ♦ 16k

United Kingdom

Joe ♦ 16k 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 COMMENT • link written 16 months ago by Joe ♦ 16k

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

ADD REPLY • link written 16 months ago by ivan.antonov • 80

16 months ago by

Pierre Lindenbaum ♦ 125k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 125k 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 COMMENT • link written 16 months ago by Pierre Lindenbaum ♦ 125k

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