How to use the hmmsearch on prototypic repetitive sequences Repbase Update database? 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 &gt; 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]
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 &gt; plantsAndFungi.ref


The, run your search on the plantsAndFungi.ref file.