A good tool for gene locus visualization

Question

Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to plug it into and get an image of the locus to compare.

I'm talking something basic like this:

score 5 · Answer 1 · answered Mar 27 '18 at 20:15

5

I think in R, Gviz is the best choice. I have used it for human sequences but it will probably also be suitable for Prokaryotes.

Another option is MS powerpoint, if you only need the arrows...

answered Mar 27 '18 at 20:15

benn

3,571
9
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yah +1 gviz is great, i've used it for bacteria – Chris_Rands Mar 27 '18 at 21:21
I wanted to avoid putting something together manually with powerpoint, even though I suspect that's how my supervisor does it... I'll take a look at Gviz though! – Mgall Mar 27 '18 at 22:04

score 3 · Answer 2 · answered Feb 05 '21 at 13:11

gggenes is a ggplot2 based solution and looks very appealing. Plus, it has a nice introduction with examples.

library(ggplot2)
library(gggenes)
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

score 3 · Answer 3 · answered Mar 28 '18 at 09:05

GFF2PS was developed for exactly this sort of thing. It takes a GFF file as input, and will produce a pretty PS output showing the annotations. It was used to create the poster for Celera's human genome draft [1].

Here's a very simple example of what it can do:

And a more complex one from the mosquito genome paper [2] (click here for a full size, 1.5M gzipped PostScript file):

If you are happy with the defaults, it is very easy to use, but otherwise it is a bit of a pain to configure. It is absurdly powerful though.

Mgall · Accepted Answer · 2019-06-20T12:36:32.657

3

I ended up using Easyfig, which is made for the task and requires little tinkering around, once fed the genbank files. (Granted, being so simple, it's hard to make the image more advanced, but it serves my purposes for now).

Here's an example of my image.

edited Jun 20 '19 at 12:36

answered Jun 15 '18 at 09:42

Mgall

101
7

Could you post an image from the software (to help future readers) ? Thanks for coming back – llrs Jun 15 '18 at 09:43

A good tool for gene locus visualization

4 Answers4