Manual

Enter an RNA sequence and optionally a secondary structure for the input sequence. If no secondary structure is entered, then the RNAbor web server computes the minimum free energy secondary structure. Enter your email (required), indicate your operating system (for file uploads). Select option to either

(A) Type/paste an RNA sequence and optionally any of the following, one per line: secondary structure for input RNA sequence, maximum base pair distance Δ from secondary structure. A FASTA comment may be given in the first line, but is not required. See explanation of input format with examples.

(B) Upload a file containing an RNA sequence with optional secondary structure and value Δ, using the same format as for typing/pasting input. A FASTA comment may be given in the first line, but is not required. See explanation of input format with examples.

For long RNA sequences, output will be returned by email. For each possible value of δ ≤ Δ, RNAbor computes the number of Boltzmann probability of all secondary structures at base pair distance δ from the minimum free energy (mfe) secondary structure.

NOTE: RNAbor run time is O(Δ*n3), so for sequences of length greater than 60, there will be a waiting time of one or more minutes, so the output will be sent by email. Sequences of at most 300 nucleotides are accepted in current web server.

Example RNA sequences.

  1. 51 nt. RNA sequence, which is the 3' untranslated regionfrom mRNA with NCBI accession code MUSGBPA.
  2. 101 nt. SAM riboswitch sequence from Rfam, with EMBL accession code AP004597.1/118941-119041. Results of RNAbor for this example are summarized here.

Output from RNAbor web engine for 51 nt. 3' UTR of mRNA MUSGBPA: