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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Quan Zou Mao-Zu Guo Yang Liu Zhi-An Xing |
| Copyright Year | 2008 |
| Description | Author affiliation: Sch. of Comput. Sci. & Technol., Harbin Inst. of Technol., Harbin (Quan Zou; Mao-Zu Guo; Yang Liu; Zhi-An Xing) |
| Abstract | Consensus RNA secondary structure and helices are always required from several homologous sequences as the development of non-coding RNA. The problem can be solved by comparative sequence analysis methods, in which nearly all the algorithms are based on multiple sequence alignment. However, there are no effective models combining similarity and secondary structure. So far multiple sequence alignment is an open problem, especially applied in predicting RNA secondary structure. In this paper, we propose a novel comparative sequence method without multiple sequence alignment. It compares the position of the helices in dot plots matrix instead of sequences. The concept 'centorid of helix' is presented and a novel algorithm is designed for finding consensus helices. Experiments on tRNA prove that our algorithm outperforms the current main software, including Pfold, MARNA, CARNAC and RNAalifold. |
| Starting Page | 29 |
| Ending Page | 33 |
| File Size | 429453 |
| Page Count | 5 |
| File Format | |
| ISBN | 9780769533049 |
| DOI | 10.1109/ICNC.2008.446 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2008-10-18 |
| Publisher Place | China |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Algorithm design and analysis Sequences RNA Biological system modeling centroid of helix pseudoknot Software algorithms RNA secondary structure prediction multiple sequence alignment Computer science Thermodynamics Hidden Markov models Biology computing comparative sequence analysis method Web server |
| Content Type | Text |
| Resource Type | Article |
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