i have suplied Farafar2 with an RNA sequences of length 47. the server returns a complete circular structure. i dont have a template and am just giving the fasta file. when i give the dot-bracket structure along with the fasta file, it returns an error too.
What is the error returned? How is the FASTA formatted? You need to make sure your dot-bracket secondary structure is the same length as the sequence.
Your fasta should look like:
for example, and your secondary structure should be 47 characters long.