Answers.Body: <p>RepBase explain what these files are on <a href="http://www.girinst.org/repbase/update/index.html" rel="nofollow noreferrer">their website</a>. It is usually a good idea to check the documentation when downloading files so you know what you're downloading. </p>
  
  <p>Based on the list of files described on the linked page, there is no <code>prirep.ref</code> file, so I assume you mean <code>plnrep.ref</code> which is "Other Plants". In any case, again according to that page, the files with plant and/or fungal data (which is what I assume you want; you never said) are:</p>
  
  <p>athrep.ref  Arabidopsis thaliana
  oryrep.ref  Oryza sativa
  dcotrep.ref Other Dicot Plants
  mcotrep.ref Other Monocot Plants
  grasrep.ref Other Grass Plants
  plnrep.ref  Other Plants
  fngrep.ref  Fungi</p>
  
  <p>There's also <code>chlrep.ref</code> for the green alga <em>Chlamydomonas reinhardtii</em>, and <code>diarep.ref</code> for the diatom <em>Thalassiosira pseudonana</em>. I don't know whether you would want to consider either here. </p>
  
  <p>In any case, since these are fasta files, you cna combine them by simply <code>cat</code>ing them together:</p>
  
  <pre><code>cat athrep.ref oryrep.ref dcotrep.ref mcotrep.ref grasrep.ref \
      plnrep.ref fngrep.ref &gt; plantsAndFungi.ref
  </code></pre>
  
  <p>The, run your search on the <code>plantsAndFungi.ref</code> file.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-12T12:32:45.753Z
Answers.Text: as I was talking to the author he mentioned that they concatenated all the files and ran a translator on nucleotide on the data. Before running the search
Answers.UserDisplayName: A.Dumas
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-11T16:13:57.067Z
Answers.LastActivityDate: 2017-12-11T16:13:57.067Z
Answers.UserDisplayName: terdon
Body: <p>I want to use the hmmsearch proposed in <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348765/" rel="nofollow noreferrer"><em>Convergence of retrotransposons in
  oomycetes and plants</em></a> by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. After the help from <a href="https://bioinformatics.stackexchange.com/a/3037/48">terdon</a> I managed to create the correct profile I assumed that the command </p>
  
  <pre><code>hmmsearch aRNH_profile.hmm prirep.ref &gt; output.out
  </code></pre>
  
  <p>would be the correct command. I downloaded the compressed database <code>RepBase22.11.fasta.tar.gz</code> from <a href="http://www.girinst.org/server/RepBase/index.php" rel="nofollow noreferrer">here</a> in the fasta format. 
  However when unpacking I get the following tree </p>
  
  <pre><code>.
  ├── angrep.ref
  ├── appendix
  │   ├── angapp.ref
  │   ├── athapp.ref
  │   ├── bctapp.ref
  │   ├── cbrapp.ref
  │  ....
  ├── athrep.ref
  ├── bctrep.ref
  ├── cbrrep.ref
  ...
  </code></pre>
  
  <p>which file is the correct fasta file? I assumed <code>prirep.ref</code>  might be correct file but the output shows </p>
  
  <pre><code>[No hits detected that satisfy reporting thresholds]
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-11T15:48:36.003Z
Comments.Text: The site requires an account in order to download. Isn't there a README or similar file explaining what each file contains? What other files are there?
   Are they all `.ref`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-11T15:59:39.300Z
Comments.Text: true. I created a account. All the files are .ref files and there is no README file
Comments.UserDisplayName: A.Dumas
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-11T16:10:18.883Z
Comments.Text: OK, so what species are you looking for? All plants? Plants and fungi? Only fungi? How about algae? What is the "correct" file for you?
Comments.UserDisplayName: terdon
Tags: <fasta><hidden-markov-models>
Title: How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?
ThreadText: # How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?
  
  (Asked by: username_0 on 2017-12-11)
  
  I want to use the hmmsearch proposed in [*Convergence of retrotransposons in
  oomycetes and plants*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348765/) by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. After the help from [username_1](https://bioinformatics.stackexchange.com/a/3037/48) I managed to create the correct profile I assumed that the command
  
  ```
  hmmsearch aRNH_profile.hmm prirep.ref > output.out
  
  ```
  
  would be the correct command. I downloaded the compressed database `RepBase22.11.fasta.tar.gz` from [here](http://www.girinst.org/server/RepBase/index.php) in the fasta format.
  However when unpacking I get the following tree
  
  ```
  .
  ├── angrep.ref
  ├── appendix
  │   ├── angapp.ref
  │   ├── athapp.ref
  │   ├── bctapp.ref
  │   ├── cbrapp.ref
  │  ....
  ├── athrep.ref
  ├── bctrep.ref
  ├── cbrrep.ref
  ...
  
  ```
  
  which file is the correct fasta file? I assumed `prirep.ref` might be correct file but the output shows
  
  ```
  [No hits detected that satisfy reporting thresholds]
  
  ```
  
  **Tags:** fasta, hidden-markov-models
  
  > **Comments:**
  > **username_1**: The site requires an account in order to download. Isn't there a README or similar file explaining what each file contains? What other files are there?  Are they all `.ref`?  
  > **username_0**: true. I created a account. All the files are .ref files and there is no README file  
  > **username_1**: OK, so what species are you looking for? All plants? Plants and fungi? Only fungi? How about algae? What is the "correct" file for you?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-12-11. Score: 1 | Accepted answer
  
  RepBase explain what these files are on [their website](http://www.girinst.org/repbase/update/index.html). It is usually a good idea to check the documentation when downloading files so you know what you're downloading.
  
  Based on the list of files described on the linked page, there is no `prirep.ref` file, so I assume you mean `plnrep.ref` which is "Other Plants". In any case, again according to that page, the files with plant and/or fungal data (which is what I assume you want; you never said) are:
  
  athrep.ref Arabidopsis thaliana
  oryrep.ref Oryza sativa
  dcotrep.ref Other Dicot Plants
  mcotrep.ref Other Monocot Plants
  grasrep.ref Other Grass Plants
  plnrep.ref Other Plants
  fngrep.ref Fungi
  
  There's also `chlrep.ref` for the green alga *Chlamydomonas reinhardtii*, and `diarep.ref` for the diatom *Thalassiosira pseudonana*. I don't know whether you would want to consider either here.
  
  In any case, since these are fasta files, you cna combine them by simply `cat`ing them together:
  
  ```
  cat athrep.ref oryrep.ref dcotrep.ref mcotrep.ref grasrep.ref \
      plnrep.ref fngrep.ref > plantsAndFungi.ref
  
  ```
  
  The, run your search on the `plantsAndFungi.ref` file.
  
  > **Comments:**
  > **username_0**: as I was talking to the author he mentioned that they concatenated all the files and ran a translator on nucleotide on the data. Before running the search  
  
  ---
  
  