<p>You can use UCSC genome browser, which supports custom genome sequence and annotation. Specifically, one needs to create a <a href="https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html" rel="nofollow noreferrer">Track Hub</a> to hold genomes and annotations. </p>

<p>Here is an example: </p>

<blockquote>
  <p><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&amp;db=hub_129615_cl_v0.8.2" rel="nofollow noreferrer">http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&amp;db=hub_129615_cl_v0.8.2</a></p>
</blockquote>

<p>And here is the corresponding <a href="http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt" rel="nofollow noreferrer">hub.txt</a> file holding the metadata, and URLs to actual fasta, bigWig and bigBed files.</p>

CC BY-SA 4.0
2018-10-12T19:24:45.873Z
2018-10-12T19:24:45.873Z
Yu Fu
<p><strong>Background</strong></p>

<p>We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a line plot:</p>

<pre><code>position score
1        5
2        6
etc.
</code></pre>

<p>Where each position corresponds to the position in the genome (i.e. FASTA).
Something like this: </p>

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

<p><strong>Question</strong></p>

<p>Is there a tool that can load a genome sequence, gene annotation, and a position ~ score file, which can be displayed as a line plot? </p>

CC BY-SA 4.0
2018-10-11T13:09:15.937Z
Welcome to the site. In order to suggest a good alternative could you comment what do you need this tool for? Why do you need to display the gene annotation? What is the problem with IGV ? (I found the sentence a bit confusing, perhaps if you rephrase it I'll understand it)
llrs
CC BY-SA 4.0
2018-10-11T13:32:33.250Z
I thought I was clear regarding what I need it for: uploading genome + annotation + own data (position + score). Why gene annotation? Because we want to look whether the the line plot we upload differs between genes and intergenic regions. Just similar as a GC plot beneath the genes and intergenic regions but then with own supplied scores per position. Indeed, I forgot a word in my sentence about IGV @Llopis
KingBoomie
CC BY-SA 4.0
2018-10-11T14:16:27.670Z
I don't find this question useful. It only helps people who find IGV ugly. Also you don't seem to have researched for other options like [IGB](https://bioviz.org/). Have a nice day!
llrs
CC BY-SA 4.0
2018-10-11T15:07:33.423Z
A local tool is fine, with upload I meant uploading it to a tool (perhaps not the best word choice). The screenshot is from a tool which only visualizes a Listeria genome (no other bacteria), but I liked the interface. Currently I'm trying to use IGB @terdon
KingBoomie
<genome><sequence-analysis><visualization>
Tool to show DNA sequence and allowing upload of own graph data
# Tool to show DNA sequence and allowing upload of own graph data

(Asked by: username_0 on 2018-10-11)

Background
We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a line plot:
position score
1        5
2        6
etc.

Where each position corresponds to the position in the genome (i.e. FASTA).
Something like this: 

Question
Is there a tool that can load a genome sequence, gene annotation, and a position ~ score file, which can be displayed as a line plot?

**Tags:** genome, sequence-analysis, visualization
> **Comments:**
> **username_1**: Welcome to the site. In order to suggest a good alternative could you comment what do you need this tool for? Why do you need to display the gene annotation? What is the problem with IGV ? (I found the sentence a bit confusing, perhaps if you rephrase it I'll understand it)  
> **username_0**: I thought I was clear regarding what I need it for: uploading genome + annotation + own data (position + score). Why gene annotation? Because we want to look whether the the line plot we upload differs between genes and intergenic regions. Just similar as a GC plot beneath the genes and intergenic regions but then with own supplied scores per position. Indeed, I forgot a word in my sentence about IGV @Llopis  
> **username_1**: I don't find this question useful. It only helps people who find IGV ugly. Also you don't seem to have researched for other options like [IGB](https://bioviz.org/). Have a nice day!  
> **username_0**: A local tool is fine, with upload I meant uploading it to a tool (perhaps not the best word choice). The screenshot is from a tool which only visualizes a Listeria genome (no other bacteria), but I liked the interface. Currently I'm trying to use IGB @terdon  

---

## 1 answers

### Answer by username_2 on 2018-10-12. Score: 1

You can use UCSC genome browser, which supports custom genome sequence and annotation. Specifically, one needs to create a [Track Hub](https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html) to hold genomes and annotations.

Here is an example:

> <http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&db=hub_129615_cl_v0.8.2>

And here is the corresponding [hub.txt](http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt) file holding the metadata, and URLs to actual fasta, bigWig and bigBed files.


---

