RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

BMC Bioinformatics

Table 6 Spearman Correlation Coefficients (r_s) of aptamer activity onto the informational complexity.

Aptamer	K_d(nM)^a	Information content(bits)
		Apt(A)^b	Apt(B)^b	Apt(C)^b	Our defined information complexity
9-4	9 ± 1	65.0	56.0	65.0	225
Class V	17 ± 4	54.5	44.5	54.5	221
10-10	30 ± 6	71.0	65.0	67.0	206
Class I	76 ± 3	45.0	41.0	45.0	136
10-59	250 ± 20	60.5	53.5	42.5	184
10-24	300 ± 50	50.0	44.0	44.0	186
9-12	300 ± 50	58.5	54.5	52.5	148
10-6	300 ± 100	71.0	65.0	67.0	186
Class II	400 ± 200	38.0	36.0	40.0	102
Class IV	900 ± 200	36.5	32.5	32.5	142
Class III	8000 ± 1000	43.5	38.5	41.5	129
r _s of K _d		0.58	0.56	0.65	0.78
*P value*		<0.050	<0.050	<0.025	<0.005

It can be seen that there is a positive correlation between the aptamer activity and the informational complexity. For more detail information of eleven GTP-bind RNAs, please refer the original paper [30] or the additional file 1.
* K_d: solution dissociation constant. (Measurement of the affinity activities of GTP-binding RNAs). The smaller the dissociation constant, the more tightly bound the ligand is, or the higher the affinity between ligand and protein. Three different methods for treating the stems were applied to calculate the aptamer information content [30]. These are indicated as Apt (A), Apt (B), and Apt(C).

ISSN: 1471-2105