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Title |
PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length
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Authors |
Xiaolan Huang1, Zhihua Du2, Jie Cheng3 & Qiang Cheng1* |
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Affiliation |
1Department of Computer Science, Southern Illinois University at Carbondale, IL 62901, USA; 2Department of Chemistry and Biochemistry, Southern Illinois University at Carbondale, IL 62901, USA; 3Department of Computer Science and Engineering, University of Hawaii at Hilo, HI 96720, USA.
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qcheng@cs.siu.edu; *Corresponding author
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Article Type |
Hypothesis
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Date |
Received March 04, 2013; Accepted March 08, 2013; Published May 25, 2013
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Abstract |
A computer program written in C++ has been developed which can detect all potential H-type RNA pseudoknots within any given RNA sequence. There is no limit on the length of the input sequence. A validation run of the program using the full-length (8173 nt) genomic mRNA of simian retrovirus type-1 (SRV-1) identifies the established -1 frameshift stimulating pseudokont at the gag-pro junction as the most stable pseudoknot within the genomic mRNA.
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Keywords |
RNA, pseudoknot, -1 ribosomal frameshifting, computational biology.
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Citation |
Huang et al.
Bioinformation 9(9): 440-442 (2013) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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Copyright |
Publisher
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Copyright Transfer Agreement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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