Table 4

Number of times that the most similar structure was produced

Method

greatest similarity to gene on

greatest similarity to gene off


RNAborMEA

18

11

RNAbor

7

11

RNAbor-Sample

2

8

RNAlocopt

3

2

RNAshapes

5

8

UNAFold

1

3


Number of times that the most similar structure to the GENE ON resp. GENE OFF structure of the B. subtilis XPT riboswitch was produced by each of the six methods investigated. Although the test was made with 34 sequences from the seed alignment of Rfam family RF00167 [31], the sums of each column may exceed 34; this is because If two or more methods produced the maximum score, then each was counted. Structural similarity was measured using the NestedAlign structural alignment algorithm [36]. While the GENE OFF structure involves a terminator loop, that is often correctly found by thermodynamics-based software, the GENE ON secondary structure, having higher free energy (hence less stable thermodynamically) is less likely to be found using thermodynamics-based approaches.

Clote et al. BMC Bioinformatics 2012 13(Suppl 5):S6   doi:10.1186/1471-2105-13-S5-S6

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