I'm trying to predict some sRNA's (small rna's) which are non-coding rna's in bacteria. I'm following an approach 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. Can someone with expertise on ncRNA's 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 do I have to do after aligning with MAUVE? I have read things like make a set of intergenic regions in BED format e and 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 have read.
Thanks in advance.
Dear Eddie Imada,
I'm also trying to predict sRNA in bacteria (in this case cyanobacteria). I've tried to use sRNAscanner, but I found some problems in creating a PWD matrix. But I think I've figured it out.
Well, I've found this review: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596055/
There are many strategies to predict sRNA. I'm still reading it. I think we can work together to create a pipeline. Hope it helps.
I have used sRNA predict and its pipeline using QRNA and other software. If you need help I can help you.
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