EMBOSS explorer

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 parameters file (optional):

Temperature

Allow GU pairs? Yes No

Allow GU pairs at end of helices? Yes No

Allow lonely pairs? Yes No

Convert T to U? Yes No

Non-standard bases

Stabilizing energies for tetra-loops? Yes No

Method BP Any with GC Any with AU parameters

Method Ignore Only unpaired bases for just one dangling end Always use dangling energies Allow coaxial stacking of adjacent helices

Method Minimum energy Partition function Both

Find sequences using only these bases

Stopping value

Number of times to search for the same structure

Continue until a match is found? Yes No

Show information for unsuccessful searches? Yes No

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