<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>

CC BY-SA 3.0
2017-12-12T12:32:45.753Z
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
A.Dumas
CC BY-SA 3.0
2017-12-11T16:13:57.067Z
2017-12-11T16:13:57.067Z
terdon
<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>

CC BY-SA 3.0
2017-12-11T15:48:36.003Z
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`?
terdon
CC BY-SA 3.0
2017-12-11T15:59:39.300Z
true. I created a account. All the files are .ref files and there is no README file
A.Dumas
CC BY-SA 3.0
2017-12-11T16:10:18.883Z
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?
terdon
<fasta><hidden-markov-models>
How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?
# 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 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]

**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. 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.

> **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  

---

