Abstract
Conventional methods for RNA 2D structure prediction search for minimal free energy structures. RNA's, however, RNA's do not always adopt global minimum structures. Rather, their structure is the result of the folding pathway followed by the structure in nature, which adopts sub-optimal folds occurring along the pathway. Our algorithm consists of an automaton that generates RNA structures by searching for optimal folding pathways. The automaton is endowed of operations to travel throughout the hyperspace of conformers embedded in a base pairing matrix. Using genetic programming it evolves optimizing its ability to find optimal pathways and finally 2D structures. Comparing the evolving automaton with conventional methods shows its potential.
| Original language | English |
|---|---|
| Title of host publication | International Joint Conference on Neural Networks 2006, IJCNN '06 |
| Pages | 2226-2233 |
| Number of pages | 8 |
| Publication status | Published - Dec 1 2006 |
| Event | International Joint Conference on Neural Networks 2006, IJCNN '06 - Vancouver, BC, Canada Duration: Jul 16 2006 → Jul 21 2006 |
Publication series
| Name | IEEE International Conference on Neural Networks - Conference Proceedings |
|---|---|
| ISSN (Print) | 1098-7576 |
Other
| Other | International Joint Conference on Neural Networks 2006, IJCNN '06 |
|---|---|
| Country | Canada |
| City | Vancouver, BC |
| Period | 7/16/06 → 7/21/06 |
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All Science Journal Classification (ASJC) codes
- Software
Cite this
An evolving automaton for RNA secondary structure prediction. / Del Carpio, Carlos A.M.; Ismael, Mohamed; Ichiishi, Eichiro; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira.
International Joint Conference on Neural Networks 2006, IJCNN '06. 2006. p. 2226-2233 1716388 (IEEE International Conference on Neural Networks - Conference Proceedings).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - An evolving automaton for RNA secondary structure prediction
AU - Del Carpio, Carlos A.M.
AU - Ismael, Mohamed
AU - Ichiishi, Eichiro
AU - Koyama, Michihisa
AU - Kubo, Momoji
AU - Miyamoto, Akira
PY - 2006/12/1
Y1 - 2006/12/1
N2 - Conventional methods for RNA 2D structure prediction search for minimal free energy structures. RNA's, however, RNA's do not always adopt global minimum structures. Rather, their structure is the result of the folding pathway followed by the structure in nature, which adopts sub-optimal folds occurring along the pathway. Our algorithm consists of an automaton that generates RNA structures by searching for optimal folding pathways. The automaton is endowed of operations to travel throughout the hyperspace of conformers embedded in a base pairing matrix. Using genetic programming it evolves optimizing its ability to find optimal pathways and finally 2D structures. Comparing the evolving automaton with conventional methods shows its potential.
AB - Conventional methods for RNA 2D structure prediction search for minimal free energy structures. RNA's, however, RNA's do not always adopt global minimum structures. Rather, their structure is the result of the folding pathway followed by the structure in nature, which adopts sub-optimal folds occurring along the pathway. Our algorithm consists of an automaton that generates RNA structures by searching for optimal folding pathways. The automaton is endowed of operations to travel throughout the hyperspace of conformers embedded in a base pairing matrix. Using genetic programming it evolves optimizing its ability to find optimal pathways and finally 2D structures. Comparing the evolving automaton with conventional methods shows its potential.
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UR - http://www.scopus.com/inward/citedby.url?scp=40649128591&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:40649128591
SN - 0780394909
SN - 9780780394902
T3 - IEEE International Conference on Neural Networks - Conference Proceedings
SP - 2226
EP - 2233
BT - International Joint Conference on Neural Networks 2006, IJCNN '06
ER -