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 RNAstrand dataset
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Robustness test: no

All RNAs from the RNAstrand dataset robustness test
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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. This ranking tests the robustness of methods predicting RNA secondary structure - if a given method did not return any prediction (i.e. because it crashed or couldn't be run on a sequence longer than a given threshold), it was assumed that according to that method a given RNA was single stranded. In this benchmark all 1987 sequences were included.
Updated: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Robustness test: yes, on all RNAs

All RNAs from the RNAstrand dataset robustness test for Rfam families
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Robustness test: yes, on RNAs with Rfam family assigned

All short RNAs from the RNAstrand dataset
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 200
Robustness test: no

All medium-sized RNAs from RNAstrand dataset
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 201, 800
Robustness test: no

All long RNAs from the RNAstrand dataset
	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 801, 30000
Robustness test: no

Pseudoknotted RNAs from RNAStrand dataset
	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Robustness test: no

Pseudoknotted short RNAs from RNAStrand dataset
	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 200
Robustness test: no

Pseudoknotted medium-sized RNAs from RNAstrand dataset
	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 201, 800
Robustness test: no

Pseudoknotted long RNAs from RNAstrand dataset
	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 801, 30000
Robustness test: no