Abstract
The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this paper, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Frank, D.N., Pace, N.R.: Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67, 153–180 (1998)
Nguyen, V.T., et al.: 7SK small nuclear RNA blinds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414, 322–325 (2001)
Yang, Z., et al.: The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414, 317–322 (2001)
Liu, C., et al.: NONCODE: an integrated knowledge database of non-coding RNAs. NAR 33(Database issue), D112–D115 (2005)
Griffiths-Jones, S., et al.: Rfam: an RNA family database. NAR 31(1), 439–441 (2003), http://www.sanger.ac.uk/Software/Rfam/
Eddy, S.: Non-coding RNA genes and the modern RNA world. Nature Reviews in Genetics 2, 919–929 (2001)
Hen, J., Greider, C.W.: Functional analysis of the pseudoknot structure in human telomerase RNA. PNAS 102(23), 8080–8085 (2005)
Dam, E., Pleij, K., Draper, D.: Structural and functional aspects of RNA pseudoknots. Biochemistry 31(47), 11665–11676 (1992)
Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.: Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45–50 (2004)
Rivas, E., Eddy, S.: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 16(7), 583–605 (2000)
Klei, R.J., Eddy, S.R.: RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics 4(1), 44 (2003)
Zhang, S., Hass, B., Eskin, E., Bafna, V.: Searching genomes for noncoding RNA using FastR. IEEE/ACM TCBBÂ 2(4) (2005)
van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., Oliehoek, J.: Pseudobase: a database with RNA pseudoknots. NAR 28(1), 201–204 (2000)
Ferre-D’Amare, A.R., Zhou, K., Doudna, J.A.: Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567–574 (1998)
Han, B., Dost, B., Bafna, V., Zhang, S.: Structural Alignment of Pseudoknotted RNA. JCB 15(5), 489–504 (2008)
Le, S.Y., Chen, J.H., Maizel, J.: Efficient searches for unusual folding regions in RNA sequences. In: Structure and Methods: Human Genome Initiative and DNA Recombination, vol. 1, pp. 127–130 (1990)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wong, T.K.F., Lam, T.W., Sung, WK., Yiu, S.M. (2009). Structural Alignment of RNA with Complex Pseudoknot Structure. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_33
Download citation
DOI: https://doi.org/10.1007/978-3-642-04241-6_33
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04240-9
Online ISBN: 978-3-642-04241-6
eBook Packages: Computer ScienceComputer Science (R0)