EMBOSS explorer


Calculate suboptimal secondary structure of RNA (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Vienna RNA structure constraints file (optional):
Vienna RNA parameters file (optional):
Advanced section
Allow circular RNA?
DOS special corrections?
Allow GU pairs?
Allow GU pairs at end of helices?
Allow lonely pairs?
Convert T to U?
Non-standard bases
Stabilizing energies for tetra-loops?
Calculate suboptimal structures within erange of the mfe
Only print structures with energy within prange of the mfe
Sort structures by energy?
Logarithmic energy function for multi-loops?
Number of random suboptimal structures
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.