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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]
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  • $\begingroup$ 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? $\endgroup$ – terdon Dec 11 '17 at 15:48
  • $\begingroup$ true. I created a account. All the files are .ref files and there is no README file $\endgroup$ – A.Dumas Dec 11 '17 at 15:59
  • $\begingroup$ 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? $\endgroup$ – terdon Dec 11 '17 at 16:10
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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.

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  • $\begingroup$ 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 $\endgroup$ – A.Dumas Dec 12 '17 at 12:32

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