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

Question

[ivan.antonov]

Hello, guys!

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

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

[Joe]

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.

[ivan.antonov]

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

[Pierre Lindenbaum]

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

[ivan.antonov]

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

[h.mon]

Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

[ivan.antonov]

Thanks for the link!

Answer 1

[h.mon]

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.

[ivan.antonov]

This is just perfect -- thanks a lot!

Answer 2

[Joe]

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

[ivan.antonov]

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

Answer 3

[Pierre Lindenbaum]

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.