Hello, I'm trying to predict some sRNA's (small rna's) which are non-coding rna's in bacteria. I'm following a aproach that i have seen in a paper, that uses MAUVE and RNAz to predict them. But the paper is not clear on protocols and i have no idea how to do this. Someone with expertise on ncRNA's can help me?

I'm trying the following: I have aligned 6 Genomes of closely related bacteria with MAUVE, and converted the output to MAF as it's the input for RNAz. Tried to run RNAz directly on this alignment but it resulted in an strange output (did not make sense to me).

My question is, what i have to do after align with MAUVE? I have read thing like make a set of intergenic regions in BED format e use it and the MAF alignment to create alignments of intergenic regions, but i have no idea how to this. Do someone know?

ps: any aproach to predict sRNA's is more than welcome, i'm only citing MAUVE because of the papers that i read.

Thanks in advance.