Title

Structural alignment of pseudoknotted RNA

Authors

Authors

B. Han; B. Dost; V. Bafna;S. J. Zhang

Comments

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Abbreviated Journal Title

J. Comput. Biol.

Keywords

dynamic programming; pseudoknotted RNA; RNA alignment; RNA secondary; structure; SECONDARY STRUCTURE; INCLUDING PSEUDOKNOTS; STRUCTURE PREDICTION; NONCODING RNAS; ALGORITHM; GENES; Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical &; Computational Biology; Statistics & Probability

Abstract

In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs.

Journal Title

Journal of Computational Biology

Volume

15

Issue/Number

5

Publication Date

1-1-2008

Document Type

Article

Language

English

First Page

489

Last Page

504

WOS Identifier

WOS:000257115500002

ISSN

1066-5277

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