<p>Your guess sounds reasonable to me but you should consider using <a href="https://github.com/DerrickWood/kraken2/wiki/Manual" rel="nofollow noreferrer">KRAKEN2</a>. You can create your custom database (you would have done it with makeblastdb anyway) and kraken will check k-mers against the database to find homologous sequences.</p>

CC BY-SA 4.0
2020-08-17T14:56:58.007Z
I don't feel Kraken is good for this task. Kraken taxonomically classifies each sequence, while the signature of integrated viral DNA will be a single sequence with both host and virus parts
Chris_Rands
CC BY-SA 4.0
2020-08-17T15:08:58.577Z
@Chris_Rands. Preparing your custom dataset with only viral genome and with the right k-length for the kmer analysis is the only method I know of existance today. You can use manually blastn (honestly, I do this myself if it's not for publication) or let the job to a well developed (and fast) software out-there. Please, let me know if you think of a better or potentially better solution!
aerijman
CC BY-SA 4.0
2020-08-17T15:25:28.007Z
Your suggestion might be fine for detecting viruses in general, but not integrated viruses specifically- this requires a fundamentally different approach because you are looking for chimeric reads
Chris_Rands
CC BY-SA 4.0
2020-08-17T15:29:18.310Z
@Chris_Rands chimeric reads could be found using shorter kmers (at the expense of dropping specificity). Do you know of any better or alternative solution?
aerijman
CC BY-SA 4.0
2020-08-15T17:44:15.247Z
2020-08-15T17:44:15.247Z
aerijman
<p>Searching directly for a reverse transcriptase may find recently incorporated retroviruses.</p>

CC BY-SA 4.0
2020-09-11T00:11:29.120Z
2020-09-11T00:11:29.120Z
Polypipe Wrangler
<p>I have an assembly of an algae and want to find if it has anything analogous to endogenous retroviruses' subsequences in its DNA.</p>
<p>My guess is I should manually blastn all subsequences until I find (or not something) that could have come from a virus.</p>
<p>Is there a better way to do this?</p>

CC BY-SA 4.0
2020-08-13T13:01:52.843Z
Is it your analysis any different to the detection of horizontal gene transfer? (Or at least I would search for this keywords for an answer)
Kamil S Jaron
CC BY-SA 4.0
2020-08-13T18:52:40.137Z
you can try with kraken: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46
aerijman
<blast><blastn>
How to find possible viral subsequences in a Eukaryote genome?
# How to find possible viral subsequences in a Eukaryote genome?

(Asked by: username_0 on 2020-08-13)

I have an assembly of an algae and want to find if it has anything analogous to endogenous retroviruses' subsequences in its DNA.

My guess is I should manually blastn all subsequences until I find (or not something) that could have come from a virus.

Is there a better way to do this?

**Tags:** blast, blastn
> **Comments:**
> **username_1**: Is it your analysis any different to the detection of horizontal gene transfer? (Or at least I would search for this keywords for an answer)  
> **username_2**: you can try with kraken: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46  

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## 2 answers

### Answer by username_2 on 2020-08-15. Score: 2

Your guess sounds reasonable to me but you should consider using [KRAKEN2](https://github.com/DerrickWood/kraken2/wiki/Manual). You can create your custom database (you would have done it with makeblastdb anyway) and kraken will check k-mers against the database to find homologous sequences.

> **Comments:**
> **username_3**: I don't feel Kraken is good for this task. Kraken taxonomically classifies each sequence, while the signature of integrated viral DNA will be a single sequence with both host and virus parts  
> **username_2**: @Chris_Rands. Preparing your custom dataset with only viral genome and with the right k-length for the kmer analysis is the only method I know of existance today. You can use manually blastn (honestly, I do this myself if it's not for publication) or let the job to a well developed (and fast) software out-there. Please, let me know if you think of a better or potentially better solution!  
> **username_3**: Your suggestion might be fine for detecting viruses in general, but not integrated viruses specifically- this requires a fundamentally different approach because you are looking for chimeric reads  
> **username_2**: @Chris_Rands chimeric reads could be found using shorter kmers (at the expense of dropping specificity). Do you know of any better or alternative solution?  

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### Answer by username_4 on 2020-09-11. Score: -1

Searching directly for a reverse transcriptase may find recently incorporated retroviruses.


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