Calculate the SNP effect on binding site and RNA fold for Bacteria

Question

[Damianos P. Melidis]

Dear all,

I would like to recalculate the effect of SNPs for the RNA fold and the binding site for bacteria genomes. I have the vcf file with SNPs comparing the isolates to the reference genome.

For the effect of SNP on RNA fold I have found:

• rnascan (https://github.com/morrislab/rnascan)
• remuRNA (https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna)

and for the effect of SNP on binding site I have found:

• prodoric (http://www.prodoric.de/index.php?index=2)

The problem is the following, for effect on RNA fold I don't know which tool is mostly used and for effect on binding site the tool that I have found can't be used through command line at my local machine.

Grateful for any help :)

Damianos