Acronyms:

• (20) - comparative methods tested on 20 sequences: 1 query + 19 random sequences takem from an Rfam seed alignment (seq id 65% <= x <= 95%) instead of all sequences from the seed alignment.
• (seed) - comparative methods tested on all sequences from the Rfam seed + the query sequence.
• RT - robustness test on all RNAs
• RT RFAM - robustness test on RNAs for which CompaRNA managed to assign an Rfam family

All RNAs from the PDB dataset standard base pair definition
	All RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. Standard base pair definition is used - it corresponds to the Leontis and Westhof classification i.e. the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry are considered as the secondary structure.
Updated: June 16, 2013
Base pair definition: standard
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Robustness test: no

Pseudoknotted RNAs standard base pair definition
	Only pseudoknotted RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. Standard base pair definition is used - it corresponds to the Leontis and Westhof classification i.e. the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry are considered as the secondary structure. Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: June 16, 2013
Base pair definition: standard
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Robustness test: no

All RNAs from the PDB dataset extended base pair definition
	All RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. The "extended" secondary structure definition includes all interacting bases using Watson-Crick, Hoogsteen or sugar edges, in both cis and trans orientations, including also base pairs conforming to the "standard" definition (the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry). Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: June 16, 2013
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Robustness test: no

Pseudoknotted RNAs extended base pair definition
	Only pseudoknotted RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. The "extended" secondary structure definition includes all interacting bases using Watson-Crick, Hoogsteen or sugar edges, in both cis and trans orientations, including also base pairs conforming to the "standard" definition (the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry). Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: June 16, 2013
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Robustness test: no