A Novel Framework Based on ACO and PSO for RNA Secondary Structure Prediction
Prediction of RNA structure is a useful process for creating new drugs and understanding genetic diseases. In this paper, we proposed a particle swarm optimization (PSO) and ant colony optimization (ACO) based framework (PAF) for RNA secondary structure prediction. PAF consists of crucial stem searc...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Hindawi Limited
2013-01-01
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| Series: | Mathematical Problems in Engineering |
| Online Access: | http://dx.doi.org/10.1155/2013/796304 |
| Summary: | Prediction of RNA structure is a useful process for creating new drugs and understanding genetic diseases. In this paper, we proposed a particle swarm optimization (PSO) and ant colony optimization (ACO) based framework (PAF) for RNA secondary structure prediction. PAF consists of crucial stem searching (CSS) and global sequence building (GSB). In CSS, a modified ACO (MACO) is used to search the crucial stems, and then a set of stems are generated. In GSB, we used a modified PSO (MPSO) to construct all the stems in one sequence. We evaluated the performance of PAF on ten sequences, which have length from 122 to 1494. We also compared the performance of PAF with the results obtained from six existing well-known methods, SARNA-Predict, RnaPredict, ACRNA, PSOfold, IPSO, and mfold. The comparison results show that PAF could not only predict structures with higher accuracy rate but also find crucial stems. |
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| ISSN: | 1024-123X 1563-5147 |