Title

Structural Alignment Of Pseudoknotted Rna

Keywords

Dynamic programming; Pseudoknotted RNA; RNA alignment; RNA secondary structure

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. © Mary Ann Liebert, Inc. 2008.

Publication Date

6-1-2008

Publication Title

Journal of Computational Biology

Volume

15

Issue

5

Number of Pages

489-504

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1089/cmb.2007.0214

Socpus ID

53049091762 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/53049091762

This document is currently not available here.

Share

COinS