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Title |
Combinatorial permutation based algorithm for representation of closed RNA secondary structures |
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Authors |
Athanasios T Alexiou*, Maria M Psiha, Panayiotis M Vlamos |
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Affiliation |
Department of Informatics, Ionian University, Plateia Tsirigoti 7, 49100 Corfu, Greece
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alexiou@ionio.gr; *Corresponding author
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Phone |
+30 6944 551797
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Fax |
+30 210 953329697
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Article Type |
Prediction Model
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Date |
Received August 22, 2011; Accepted August 30, 2011; Published September 06, 2011
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Abstract |
A permutation-based algorithm is introduced for the representation of closed RNA secondary structures. It is an efficient ‘loopless’ algorithm, which generates the permutations on base-pairs of ‘k-noncrossing’ setting partitions. The proposed algorithm reduces the computational complexity of known similar techniques in O(n), using minimal change ordering and transposing of not adjacent elements.
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Keywords |
Closed RNA secondary structures, k-noncrossing partitions, permutation-based algorithm
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Citation |
Alexiou et al.
Bioinformation 7(2): 91-95 (2011) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |