<p>I have a gbk files for a viral genome that I have used biopython to add features of the <code>3'</code> and <code>5'</code> <code>UTRs</code>. However when looking in a genome viewer (IGV) I don't see these features. I am not unsure if I encoded the UTR features into the gbk file correctly.</p>
<p>They look like this for example:</p>
<pre><code>5'UTR           39..104
3'UTR           961..2956
5'UTR           1098..1126
3'UTR           2781..2956
5'UTR           3138..3193
3'UTR           6594..7013
5'UTR           15611..15770
3'UTR           16996..17054
5'UTR           complement(17856..17960)
3'UTR           complement(17164..17243)
5'UTR           complement(19557..21099)
</code></pre>
<p>Whole gbk file <a href="http://pastebin.com/8jm2LEk2" rel="nofollow noreferrer">here</a></p>
<p>I encoded them in the following way:</p>
<pre><code>   seqID = some-gene_name
   Start = SeqFeature.ExactPosition(some_number)
   End = SeqFeature.ExactPosition(some_number)
   seqStrand = 1 #or -1
   FeatureLoc = SeqFeature.FeatureLocation(Start, End)
   Feature = SeqFeature.SeqFeature(FeatureLoc, type = &quot;5'UTR&quot;, strand = seqStrand, id =seqID)
</code></pre>
<p>I have also tried converting the gbk into a gff file and the line concerning the UTR's look like:</p>
<pre><code>GQ994935.1  feature 5'UTR   39  104 .   +   .   
GQ994935.1  feature 3'UTR   961 2956    .   +   .   
GQ994935.1  feature 5'UTR   1098    1126    .   +   .   
GQ994935.1  feature 3'UTR   2781    2956    .   +   .   
GQ994935.1  feature 5'UTR   3138    3193    .   +   .   
GQ994935.1  feature 3'UTR   6594    7013    .   +   .   
GQ994935.1  feature 5'UTR   15611   15770   .   +   .   
GQ994935.1  feature 3'UTR   16996   17054   .   +   .   
GQ994935.1  feature 5'UTR   17856   17960   .   -   .   
GQ994935.1  feature 3'UTR   17164   17243   .   -   .   
GQ994935.1  feature 5'UTR   19557   21099   .   -   .   
GQ994935.1  feature 3'UTR   18576   18590   .   -   .   
GQ994935.1  feature 5'UTR   21051   21099   .   -   .   
GQ994935.1  feature 3'UTR   18576   20039   .   -   .   
</code></pre>
<p>This is what I see in IGV:
<a href="https://i.sstatic.net/0M2Sv.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0M2Sv.png" alt="enter image description here" /></a></p>
<p>THis is just the regular CDS features with no UTRs</p>
<p>Am I doing this incorrectly?</p>
<hr />
<p><strong>Summary</strong> from comments</p>
<p>The gff3 file has been inspected (presented above), however it remains uncertain how the UTR regions should be represented. The intention is for the UTR regions represented as a features the same as a CDS.</p>
<p>The information copied and pasted is an excerpt from the gbk file, with supporting information from GFF files as requested (below). The formatted described is the Biopython output.</p>
<p>Further information is here: <a href="http://pastebin.com/8jm2LEk2" rel="nofollow noreferrer">http://pastebin.com/8jm2LEk2</a></p>

CC BY-SA 4.0
2020-10-21T09:49:28.200Z
What file are you loading into IGV? how are you expecting to see the UTRs? What do you actually see instead? Please [edit] your question and clarify.
terdon
CC BY-SA 4.0
2020-10-21T14:11:21.393Z
@terdon I have looked at the gff3 file, I am unsure what to expect as I don't know how utr regions are represented but my wish is to see the urt regions represented as a features the same as a CDS. Instead I just see nothing but the normal CDS features
Lamma
CC BY-SA 4.0
2020-10-21T14:14:04.743Z
Please [edit] your question and i) explain that you are loading a gff3 file into IGV; ii) show us a few lines of this file so we know what you are doing and iii) include a screenshot of what you see in IGV; iv) clarify if you are working with genbank files or gff files. What are the first lines in your question? They look like they come from a genbank file, but those lines alone are no known format. Is that what you're using?
terdon
CC BY-SA 4.0
2020-10-22T06:28:05.070Z
@terdon. I have tried with both gbk and gff3. What is pasted is just an excerpt from the gbk file (I will add gff also). The format is just that produced by biopython so I am unsure about it being "no known format" as I don't know what the format should look like. Yes that is what i am using :)
Lamma
CC BY-SA 4.0
2020-10-22T08:17:58.357Z
I still don't understand what file you are loading in IGV. Is that gff file what you load? The one that _only_ contains UTRs? Or do you load the first file you show, the incomplete genbank file? Can you please give us an example of the actual file you load into UGVIGV?
terdon
CC BY-SA 4.0
2020-10-22T11:38:28.780Z
@terdon I am have tried viewing the gbk file in IGV which is what I have shown above. the gbk and gff contain all the original CDS features but I have just added in the UTRs. here is the complete gbk file I am using: https://pastebin.com/8jm2LEk2
Lamma
CC BY-SA 4.0
2020-10-23T11:26:09.030Z
The UTRs display properly in SnapGene or in https://cuba.genomefoundry.org/plot-sequence-features so the problem must be an IGV setting
Peter
CC BY-SA 4.0
2020-10-23T14:28:51.317Z
@Peter Youa re correct, seems to be a IGV error
Lamma
<python><sequence-annotation><covid-19><genbank><virus>
UTR features in gbk files
# UTR features in gbk files

(Asked by: username_0 on 2020-10-20)

I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' UTRs. However when looking in a genome viewer (IGV) I don't see these features. I am not unsure if I encoded the UTR features into the gbk file correctly.
They look like this for example:
5'UTR           39..104
3'UTR           961..2956
5'UTR           1098..1126
3'UTR           2781..2956
5'UTR           3138..3193
3'UTR           6594..7013
5'UTR           15611..15770
3'UTR           16996..17054
5'UTR           complement(17856..17960)
3'UTR           complement(17164..17243)
5'UTR           complement(19557..21099)

Whole gbk file here
I encoded them in the following way:
   seqID = some-gene_name
   Start = SeqFeature.ExactPosition(some_number)
   End = SeqFeature.ExactPosition(some_number)
   seqStrand = 1 #or -1
   FeatureLoc = SeqFeature.FeatureLocation(Start, End)
   Feature = SeqFeature.SeqFeature(FeatureLoc, type = "5'UTR", strand = seqStrand, id =seqID)

I have also tried converting the gbk into a gff file and the line concerning the UTR's look like:
GQ994935.1  feature 5'UTR   39  104 .   +   .   
GQ994935.1  feature 3'UTR   961 2956    .   +   .   
GQ994935.1  feature 5'UTR   1098    1126    .   +   .   
GQ994935.1  feature 3'UTR   2781    2956    .   +   .   
GQ994935.1  feature 5'UTR   3138    3193    .   +   .   
GQ994935.1  feature 3'UTR   6594    7013    .   +   .   
GQ994935.1  feature 5'UTR   15611   15770   .   +   .   
GQ994935.1  feature 3'UTR   16996   17054   .   +   .   
GQ994935.1  feature 5'UTR   17856   17960   .   -   .   
GQ994935.1  feature 3'UTR   17164   17243   .   -   .   
GQ994935.1  feature 5'UTR   19557   21099   .   -   .   
GQ994935.1  feature 3'UTR   18576   18590   .   -   .   
GQ994935.1  feature 5'UTR   21051   21099   .   -   .   
GQ994935.1  feature 3'UTR   18576   20039   .   -   .   

This is what I see in IGV:

THis is just the regular CDS features with no UTRs
Am I doing this incorrectly?

Summary from comments
The gff3 file has been inspected (presented above), however it remains uncertain how the UTR regions should be represented. The intention is for the UTR regions represented as a features the same as a CDS.
The information copied and pasted is an excerpt from the gbk file, with supporting information from GFF files as requested (below). The formatted described is the Biopython output.
Further information is here: http://pastebin.com/8jm2LEk2

**Tags:** python, sequence-annotation, covid-19, genbank, virus
> **Comments:**
> **username_1**: What file are you loading into IGV? how are you expecting to see the UTRs? What do you actually see instead? Please [edit] your question and clarify.  
> **username_0**: @terdon I have looked at the gff3 file, I am unsure what to expect as I don't know how utr regions are represented but my wish is to see the urt regions represented as a features the same as a CDS. Instead I just see nothing but the normal CDS features  
> **username_1**: Please [edit] your question and i) explain that you are loading a gff3 file into IGV; ii) show us a few lines of this file so we know what you are doing and iii) include a screenshot of what you see in IGV; iv) clarify if you are working with genbank files or gff files. What are the first lines in your question? They look like they come from a genbank file, but those lines alone are no known format. Is that what you're using?  
> **username_0**: @terdon. I have tried with both gbk and gff3. What is pasted is just an excerpt from the gbk file (I will add gff also). The format is just that produced by biopython so I am unsure about it being "no known format" as I don't know what the format should look like. Yes that is what i am using :)  
> **username_1**: I still don't understand what file you are loading in IGV. Is that gff file what you load? The one that _only_ contains UTRs? Or do you load the first file you show, the incomplete genbank file? Can you please give us an example of the actual file you load into UGVIGV?  
> **username_0**: @terdon I am have tried viewing the gbk file in IGV which is what I have shown above. the gbk and gff contain all the original CDS features but I have just added in the UTRs. here is the complete gbk file I am using: https://pastebin.com/8jm2LEk2  
> **username_2**: The UTRs display properly in SnapGene or in https://cuba.genomefoundry.org/plot-sequence-features so the problem must be an IGV setting  
> **username_0**: @Peter Youa re correct, seems to be a IGV error  

---

## 0 answers

