How to visualize gene structure of a (prokaryotic) locus?
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3.1 years ago
ivan.antonov ▴ 90

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

R genome gene visualisation python • 1.7k views
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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.

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

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

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

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Some suggestions at an old thread:

Are There Any Scripts That Make Images From Gff Files?

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Thanks for the link!

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3.1 years ago
h.mon 33k

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.

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This is just perfect -- thanks a lot!

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3.1 years ago
Joe 19k

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

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

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3.1 years ago

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.

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