text: user2026: I want to use the hmmsearch proposed in Convergence of retrotransposons in
  oomycetes and plants by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. After the help from terdon 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 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]
  
  
  user298: RepBase explain what these files are on their website. 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 cating 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.
  
original_text: 2026: <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>
   298: <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>
  