Answers.Body: <p>I have BLASTed one of the tRNA sequences. Lactobacillus acidophilus, Ile, that has insertion sites.</p>
  <blockquote>
  <p>GGGCCTATAGCTCAGCTGGTTTAGAGC_CACGCCTGATAAGCGTG_GTCGATGGTTCAAGTCCATTTAGGCCCA</p>
  </blockquote>
  <p>It looks like insertion refers to sites that exist in reference DNA but missing from tRNA sequence. But I am not a tRNA expert, it's my interpretation. See the image.
  <a href="https://i.sstatic.net/eaCZR.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/eaCZR.png" alt="enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-25T15:43:46.820Z
Answers.LastActivityDate: 2022-02-25T15:43:46.820Z
Answers.UserDisplayName: Supertech
Answers.Body: <p>I post the workaround that I eventually found for this problem as it could serve as a reference for the exploration of <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/" rel="nofollow noreferrer">tRNAdb</a> bioinformatic resource.
  <a href="https://i.sstatic.net/JSDkF.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/JSDkF.png" alt="Just a screen shot for tdbR0000042" /></a></p>
  <p>If you look at the picture, <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/" rel="nofollow noreferrer">tRNAdb</a> provides comments about the insertion symbols. Therefore, for the specified position, nucleotides are defined. The original tRNA sequences can be reconstructed from this information.
  Hope that this problem could be of help to the community!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-09T12:55:42.223Z
Answers.LastActivityDate: 2022-03-09T12:55:42.223Z
Answers.UserDisplayName: Spartan 117
Body: <p>I have to manually curate some tRNA sequences in order to have their original sequence without modifications. I am getting these sequences from <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/Welcome" rel="nofollow noreferrer">tRNAdb</a>. In these sequences, I found often &quot;<strong>_</strong>&quot; symbols.
  They provide this <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf" rel="nofollow noreferrer">list</a> of symbols and &quot;_&quot; corresponds to <em>insertion</em>. My question is the insertion of what? Are they referring to a reference sequence? In the <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf" rel="nofollow noreferrer">list</a> they say that in the footnotes they provide more info. However, there are no footnotes.
  Have you ever had experience with tRNAdb?</p>
  
Tags: <trna>
Title: tRNAdb insertion symbols. To what they correspond?
ThreadText: # tRNAdb insertion symbols. To what they correspond?
  
  (Asked by: username_0 on 2022-02-25)
  
  I have to manually curate some tRNA sequences in order to have their original sequence without modifications. I am getting these sequences from [tRNAdb](http://trna.bioinf.uni-leipzig.de/DataOutput/Welcome). In these sequences, I found often "**\_**" symbols.
  They provide this [list](http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf) of symbols and "\_" corresponds to *insertion*. My question is the insertion of what? Are they referring to a reference sequence? In the [list](http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf) they say that in the footnotes they provide more info. However, there are no footnotes.
  Have you ever had experience with tRNAdb?
  
  **Tags:** trna
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2022-02-25. Score: 3
  
  I have BLASTed one of the tRNA sequences. Lactobacillus acidophilus, Ile, that has insertion sites.
  
  > GGGCCTATAGCTCAGCTGGTTTAGAGC\_CACGCCTGATAAGCGTG\_GTCGATGGTTCAAGTCCATTTAGGCCCA
  
  It looks like insertion refers to sites that exist in reference DNA but missing from tRNA sequence. But I am not a tRNA expert, it's my interpretation. See the image.
  [![enter image description here](https://i.sstatic.net/eaCZR.png)](https://i.sstatic.net/eaCZR.png)
  
  
  ---
  
  ### Answer by username_0 on 2022-03-09. Score: 0
  
  I post the workaround that I eventually found for this problem as it could serve as a reference for the exploration of [tRNAdb](http://trna.bioinf.uni-leipzig.de/DataOutput/) bioinformatic resource.
  [![Just a screen shot for tdbR0000042](https://i.sstatic.net/JSDkF.png)](https://i.sstatic.net/JSDkF.png)
  
  If you look at the picture, [tRNAdb](http://trna.bioinf.uni-leipzig.de/DataOutput/) provides comments about the insertion symbols. Therefore, for the specified position, nucleotides are defined. The original tRNA sequences can be reconstructed from this information.
  Hope that this problem could be of help to the community!
  
  
  ---
  
  