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Table 1 Designable RNA secondary structures

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

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

  1. 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.
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Algorithms for Molecular Biology

ISSN: 1748-7188