D−ORB

Make the first sequence(s) mandatory for ORBs and consensus structure
Keep duplicated sequences (removed by default) (will also apply to submitted negative sequences)

Negative sequences

Also use 50% of randomly and uniformly distributed Rfam seed sequences

Landscape

MC-Flashfold + MC-Convergence
Submit your own secondary structures in dot-bracket notation

File must be in FASTA format with mandatory headers matching the headers of submitted sequences, and the secondary structures of each sequence in dot-bracket (.) format, one structure per line:


>positive1
((...))
(.....)
>positive2
((...))
(.....)
>negative1
((...))
(.....)

Abstract shape

Let D-ORB determine the abstract shape
Submit the abstract shape

Position offset nucleotides (leave it at 0 if the first nucleotide starts at 1)

D-ORB

The Overrepresented RNA Blocks