@inproceedings{d4d3563419fc4c4f840698ae06178c78,
title = "Structural alignment of RNA with complex pseudoknot structure",
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.",
keywords = "Non-coding RNA, Pseudoknots, Structural alignment",
author = "Wong, {Thomas K.F.} and Lam, {T. W.} and Sung, {Wing Kin} and Yiu, {S. M.}",
year = "2009",
doi = "10.1007/978-3-642-04241-6_33",
language = "English",
isbn = "3642042406",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "403--414",
booktitle = "Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings",
note = "9th International Workshop on Algorithms in Bioinformatics, WABI 2009 ; Conference date: 12-09-2009 Through 13-09-2009",
}