Table 3.

Comparisons with literature sets

Set name	Word number length	PM ΔG (T1)		MM ΔG (T2) min	Tm range (T5)		ρ	δ	δ*	Δ	CombFold	τ	τ*	Match		Mismatch
		Min	Max		Min	Max
S1Braich	40	−16.80	−13.57	−9.29	46.64	55.75	9.11	6.25	4.28	354.33	−1.25	4.10	1.84	w14	c14	w14	c4
S1 Shortreed	15mers	−15.22	−13.71	−7.29	47.01	49.98	2.97	7.20	6.42	5418.59	−2.47	7.03	5.81	w8	c8	w38	c8
S2 Brenner	8	−1.97	−1.01	−1.86	−67.19	−48.07	19.12	−0.19	−0.85	0.73				w1	c1	w1	c3
S2 Shortreed	4mers	−1.51	−1.01	−0.67	−67.19	−49.66	17.53	0.39	0.34	1.88				w6	c6	w6	c8
S4 Frutos	108	−8.95	−6.50	−8.72	17.06	27.34	10.28	−0.33	−2.22	0.61				w4	c4	w3	w4
S4 Shortreed	8mers	−8.59	−6.50	−6.70	17.06	25.78	8.72	1.35	−0.20	8.90				w59	c59	w12	c59
S5 Penchovsky	24	−17.94	−16.84	−8.72	55.15	58.65	3.50	8.79	8.12	3570.05	0.00	6.88	5.78	w22	c22	w22	c11
S5 Shortreed	16mers	−17.75	−17.05	−7.91	56.07	57.41	1.34	9.34	9.14	10842.11	−0.77	8.32	8.06	w16	c16	w16	c19
S7 Tulpan	64	−13.24	−12.54	−8.89	42.41	43.48	1.07	3.72	3.65	95.59	0.00	0.23	−0.64	w54	c54	w54	c64
S7 Shortreed	12mers	−12.66	−11.78	−8.94	42.38	43.50	1.12	2.87	2.84	23.20	−1.03	2.91	2.76	w14	c14	w14	c19
S8 Tulpan	64	−16.98	−15.70	−7.61	51.81	52.75	0.94	8.15	8.09	9816.31	−2.52	3.55	3.49	w56	c56	w3	c56
S8 Shortreed	16mers	−16.42	−15.45	−7.62	51.81	52.77	0.96	8.11	7.83	4740.07	−5.50	5.59	5.25	w12	c12	w12	c36
S8 Tulpan (10 C)	64	−25.45	−24.19	−14.30	51.81	52.75	0.94	10.04	9.89	10606.99	−16.93	4.17	3.75	w64	c64	w64	c13
S8 Shortreed (10 C)	16mers	−25.22	−24.12	−11.65	51.81	52.77	0.96	13.02	12.47	106597.39	−12.07	9.21	8.37	w11	c11	w19	c11

Six pairwise comparisons were made between sets created using the algorithm described here and sets created using other published algorithms. Sets were named according to the first author of the work and also by (S1–S8) to match nomenclature used in the accompanying manuscript. All free energies are in kcal/mol and all temperatures are in °C. T1 contains values for the minimum and maximum free energy for perfectly complementary duplexes w_ic_i; T2 contains the free energy of the most stable mismatch between words and complements (w_ic_j or w_jc_i); T5 contains values for the minimum and maximum melting temperatures for all perfectly complementary duplexes in the set; ρ is the width of the melting temperature range; δ and δ* refer to free energy differences between perfect matches and mismatches (see Equation 1 and the accompanying text); Δ refers to the discrimination factor (Equation 8); CombFold is the minimum free energy for the most stable secondary structure, which is formed when individual words are concatenated together for the formation of the combinatorial library; τ and τ* refer to free energies associated with mishybridization between word complements and word-word junctions (see Equation 10 and the accompanying text). Vacant table entries for the Brenner and Frutos sets are because words in these sets were not designed with concatenation in mind. The columns with the headings ‘match’ and ‘mismatch’ contain the identities of the sequences with the narrowest gap in free energy between a perfect match hybridization and a mismatch hybridization.