EMBOSS explorer

RNAalifold

Calculate secondary structures for a set of aligned RNAs (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
Temperature
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?
Circular RNA?
Colour structure plot?
Method
Estimate of ensemble free energy
Method
Weight for covariance
Non-compatible sequence penalty
Mark end gaps?
Use most informative sequence algorithm?
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.