Name
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 pseudo-knotted 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 finds two appli- cations. First, by scanning a genome, we can identify novel (homologous) pseu- doknotted 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 pseu- doknots. 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. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1007/11732990_13 | Research in Computational Molecular Biology |
Keywords | DocType | Volume |
entire viral genome,pseudo-knotted structure,rna sequence,novel homologs,secondary structure,pseudoknotted ncrna,ncrna family,structural alignment,primary sequence,efficient algorithm,pseudoknotted rna,mouse genome,structure alignment,non coding rna | Conference | 3909 |
ISSN | ISBN | Citations |
0302-9743 | 3-540-33295-2 | 10 |
PageRank | References | Authors |
0.62 | 13 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Banu Dost | 1 | 92 | 5.09 |
| Buhm Han | 2 | 50 | 8.89 |
| Shaojie Zhang | 3 | 203 | 28.81 |
| Vineet Bafna | 4 | 1967 | 226.80 |