<p>I ended up using <a href="http://mjsull.github.io/Easyfig/" rel="nofollow noreferrer">Easyfig</a>, 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).</p>

<p><a href="https://i.sstatic.net/ARj7n.gif" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ARj7n.gif" alt="Easyfig example from the homepage."></a></p>

<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498615/bin/12864_2019_5692_MOESM4_ESM.pdf" rel="nofollow noreferrer">Here's an example of my image.</a></p>

CC BY-SA 4.0
2018-06-15T09:42:30.913Z
2019-06-20T12:36:32.657Z
2019-06-20T12:36:32.657Z
Mgall
<p>I think in R, <a href="https://bioconductor.org/packages/release/bioc/html/Gviz.html" rel="noreferrer">Gviz</a> is the best choice. I have used it for human sequences but it will probably also be suitable for Prokaryotes.</p>

<p>Another option is MS powerpoint, if you only need the arrows...</p>

CC BY-SA 3.0
2018-03-27T21:21:57.183Z
yah +1 gviz is great, i've used it for bacteria
Chris_Rands
CC BY-SA 3.0
2018-03-27T22:04:53.750Z
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
CC BY-SA 3.0
2018-03-27T20:15:46.607Z
2018-03-27T20:15:46.607Z
benn
<p><a href="http://big.crg.cat/services/gff2ps" rel="nofollow noreferrer">GFF2PS</a> 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 <a href="http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2" rel="nofollow noreferrer">the poster</a> for Celera's human genome draft <a href="http://www.sciencemag.org/cgi/content/abstract/291/5507/1304" rel="nofollow noreferrer">[1]</a>. </p>

<p>Here's a very simple example of what it can do:</p>

<p><a href="https://i.sstatic.net/DrQxG.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/DrQxG.png" alt="gff2ps example"></a></p>

<p>And a more complex one from the mosquito genome paper <a href="http://www.sciencemag.org/cgi/content/abstract/298/5591/129" rel="nofollow noreferrer">[2]</a> (click <a href="http://genome.imim.es/references/genome_maps/2002_Science_v298_i5591_p129_fig1_MosquitoGenome.ps.gz" rel="nofollow noreferrer">here</a> for a full size, 1.5M gzipped PostScript file):</p>

<p><a href="https://i.sstatic.net/twKYV.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/twKYV.jpg" alt="anopheles gambiae genome"></a></p>

<p>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. </p>

<hr>

<ol>
<li><a href="http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2" rel="nofollow noreferrer">Venter et al. Science 291(5507):1304-1351 (2001)</a></li>
<li><a href="http://www.sciencemag.org/cgi/content/abstract/298/5591/129" rel="nofollow noreferrer">Holt et al. Science 298(5591):129-149 (2002)</a></li>
</ol>

CC BY-SA 3.0
2018-03-28T09:05:21.113Z
2018-03-28T09:05:21.113Z
terdon
<p><a href="https://github.com/wilkox/gggenes/" rel="nofollow noreferrer">gggenes</a> is a ggplot2 based solution and looks very appealing. Plus, it has a nice introduction with <a href="https://wilkox.org/gggenes/articles/introduction-to-gggenes.html" rel="nofollow noreferrer">examples</a>.</p>
<pre class="lang-r prettyprint-override"><code>library(ggplot2)
library(gggenes)
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  facet_wrap(~ molecule, scales = &quot;free&quot;, ncol = 1) +
  scale_fill_brewer(palette = &quot;Set3&quot;) +
  theme_genes()
</code></pre>
<p><img src="https://wilkox.org/gggenes/articles/introduction-to-gggenes_files/figure-html/theme_genes-1.png" alt="" /></p>

CC BY-SA 4.0
2021-02-05T13:11:45.763Z
2021-02-05T13:11:45.763Z
Alex
<p>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.</p>

<p>I'm talking something basic like this:</p>

<p><a href="https://i.sstatic.net/CPGkw.gif" rel="noreferrer"><img src="https://i.sstatic.net/CPGkw.gif" alt="enter image description here"></a></p>

<gene><visualization>
A good tool for gene locus visualization
# A good tool for gene locus visualization

(Asked by: username_0 on 2018-03-27)

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:

[![enter image description here](https://i.sstatic.net/CPGkw.gif)](https://i.sstatic.net/CPGkw.gif)

**Tags:** gene, visualization

---

## 4 answers

### Answer by username_0 on 2018-06-15. Score: 3 | Accepted answer

I ended up using [Easyfig](http://mjsull.github.io/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).

[![Easyfig example from the homepage.](https://i.sstatic.net/ARj7n.gif)](https://i.sstatic.net/ARj7n.gif)

[Here's an example of my image.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498615/bin/12864_2019_5692_MOESM4_ESM.pdf)


---

### Answer by username_1 on 2018-03-27. Score: 5

I think in R, [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html) 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...

> **Comments:**
> **username_2**: yah +1 gviz is great, i've used it for bacteria  
> **username_0**: 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!  

---

### Answer by username_3 on 2018-03-28. Score: 4

[GFF2PS](http://big.crg.cat/services/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](http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2) for Celera's human genome draft [[1]](http://www.sciencemag.org/cgi/content/abstract/291/5507/1304).

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

[![gff2ps example](https://i.sstatic.net/DrQxG.png)](https://i.sstatic.net/DrQxG.png)

And a more complex one from the mosquito genome paper [[2]](http://www.sciencemag.org/cgi/content/abstract/298/5591/129) (click [here](http://genome.imim.es/references/genome_maps/2002_Science_v298_i5591_p129_fig1_MosquitoGenome.ps.gz) for a full size, 1.5M gzipped PostScript file):

[![anopheles gambiae genome](https://i.sstatic.net/twKYV.jpg)](https://i.sstatic.net/twKYV.jpg)

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.

---

1. [Venter et al. Science 291(5507):1304-1351 (2001)](http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2)
2. [Holt et al. Science 298(5591):129-149 (2002)](http://www.sciencemag.org/cgi/content/abstract/298/5591/129)


---

### Answer by username_4 on 2021-02-05. Score: 3

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()


---

