An image processing approach to computing distances between RNA secondary structures dot plots

Table 1 Designable RNA secondary structures

Index	Structure in dot-brackets notation	Length (nt.)	Output sequence of original RNAinverse [6]	Output sequence of modified RNAinverse [6]
1	(((...(((...(((...)))...(((...)))...)))...)))	45	ACCGCCAGACAGGGCCAAGCCA-	UCCAAAUUCAUAGUAUAAUACA-
			CAUCCUAAGGAAAAGAAAAAGGA	CAUCCUAAGGAAAAGAAAAAGGA
2	(((.((.(((..((((((((.......)))))))))))...)).)))	47	GCUGUAGCCAAGUGGUAGUUGCU-	GCGUUCCGUCAGACUCAUGAGGC-
			AUAAAAUUAUUAUGGAUGUAGGGU	UAGGUCAUGGGUGACUCAGACCGC
3	(((((..((....((((.....)))).....))...)))))	41	GUCUGAAGCUCAAUGAUCUC-	CUAGACCUCUUUAGUGGAAC-
			CAAUUAAACUCGUGUACGGAU	GGCCGCGGACUGAAUAUCUAG
4	.((((((((((((...((.......))...))))))))).)))	43	CUCGUGAAUAUAACACUCAAG-	AUUCAAAAAAAACAAAUCAAA-
			GACCGAAAUUUAUGUUUAGUGA	AAAAGAAAAGUUUUUUUUAGAA
5	((((..(((...((...(((((....)))))...))...)))))))	46	GGUUCAGUUCAUUGCUCAUACUU-	UAUGUUAUCAAUUGUUGGCAUGC-
			AACGGUAUUCUCGUACGACAACC	AGUCAUGCAUUCAUAGGGUCGUG

This table displays the results for five designable secondary structures, comparing the original RNAinverse (using base pairing distance) output sequence, with the modified RNAinverse (using our proposed DoPloCompare distance) output sequence. Both algorithms succeeded in designing a sequence that folds into the input secondary structures, depicted in the second column, thus providing sequences with zero distance to the input structure.

ISSN: 1748-7188