Answers.Body: <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>
  
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Answers.CreationDate: 2020-08-17T14:56:58.007Z
Answers.Text: 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
Answers.UserDisplayName: Chris_Rands
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Answers.CreationDate: 2020-08-17T15:08:58.577Z
Answers.Text: @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 You can use manually blastn (honestly, I do this myself if it's not for publication) or let the job to a well developed (and fast) software out-there.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!
Answers.UserDisplayName: aerijman
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Answers.CreationDate: 2020-08-17T15:25:28.007Z
Answers.Text: 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
Answers.UserDisplayName: Chris_Rands
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Answers.CreationDate: 2020-08-17T15:29:18.310Z
Answers.Text: @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?
Answers.UserDisplayName: aerijman
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Answers.CreationDate: 2020-08-15T17:44:15.247Z
Answers.LastActivityDate: 2020-08-15T17:44:15.247Z
Answers.UserDisplayName: aerijman
Answers.Body: <p>Searching directly for a reverse transcriptase may find recently incorporated retroviruses.</p>
  
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Answers.CreationDate: 2020-09-11T00:11:29.120Z
Answers.LastActivityDate: 2020-09-11T00:11:29.120Z
Answers.UserDisplayName: Polypipe Wrangler
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-13T13:01:52.843Z
Comments.Text: 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)
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-13T18:52:40.137Z
Comments.Text: you can try with kraken: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46
Comments.UserDisplayName: aerijman
Tags: <blast><blastn>
Title: How to find possible viral subsequences in a Eukaryote genome?
ThreadText: # 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  
  
  ---
  
  ## 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**: @username_3. 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**: @username_3 chimeric reads could be found using shorter kmers (at the expense of dropping specificity). Do you know of any better or alternative solution?  
  
  ---
  
  ### Answer by username_4 on 2020-09-11. Score: -1
  
  Searching directly for a reverse transcriptase may find recently incorporated retroviruses.
  
  
  ---
  
  