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]