<p>I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene <em><strong>X</strong></em> is located on scaffold 1234, from nucleotide 1 - 2250, while gene <em><strong>Y</strong></em> is located on scaffold 2571, from nucleotide 3380 - 5790.</p>
<p>Given this information is it possible to determine if these genes are close to each other in the genome?</p>
<p>Many thanks for your help,</p>
<ul>
<li>Leah</li>
</ul>

CC BY-SA 4.0
2020-04-03T09:49:55.573Z
great question.. i guess if you cannot assemble the contigs, chances are you are unlikely to get it from the current dataset.. which organism is this?
StupidWolf
CC BY-SA 4.0
2020-04-04T18:57:50.630Z
Thanks @StupidWolf! It is a wgs from an amoebozoan protist.
Leah
CC BY-SA 4.0
2020-04-04T19:03:41.060Z
@michael, I would very much appreciate your thoughts on this question!
Leah
<genome><wgs><scaffold>
Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?
# Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

(Asked by: username_0 on 2020-04-03)

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene ***X*** is located on scaffold 1234, from nucleotide 1 - 2250, while gene ***Y*** is located on scaffold 2571, from nucleotide 3380 - 5790.

Given this information is it possible to determine if these genes are close to each other in the genome?

Many thanks for your help,

* Leah

**Tags:** genome, wgs, scaffold
> **Comments:**
> **username_1**: great question.. i guess if you cannot assemble the contigs, chances are you are unlikely to get it from the current dataset.. which organism is this?  
> **username_0**: Thanks @StupidWolf! It is a wgs from an amoebozoan protist.  
> **username_0**: @michael, I would very much appreciate your thoughts on this question!  

---

## 0 answers

