Dear,
I performed a multi-sequence alignment (MSA) with all the complete genome sequences of SARS-related viruses. I then used RNALalifold from the ViennaRNA package, with default parameters, to determine the boundaries of locally stable structures within MSA, and realigned these local regions using LocARNA. Later, I assessed the significance and conservation of the structures found with RNAz and now, I'm in search of an ab initio software/method to predict pre-miRNAs using the structured regions detected by RNAz as input.
I'm looking forward to your kind comments.
I think Vmir will help you with predicting pre-miRNAs, please chek the paper for more details. I used years ago, I simply needs the viral genome fasta file and produce a file with candidate per-miRNAs.
Article Computational Prediction of Viral miRNAs
Musa Mohammadi Thanks for you reply, but Vmir does work on windows OS and I really don't have anywhere to run it. I would like a Linux based software.
Alexis Felipe Rojas Cruz I'm also using Linux based distro (Ubuntu 20.04), to used I tried to install vmir with Winehq but it seems it's not compatible with this way of running windows based programs. So to solve this problem I just used virtual machine (VirtualBox) with windows 7 and it worked for me. You just need to find some windows 7 iso file.
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