Name
Abstract | ||
|---|---|---|
With the growing number of known RNA genes efficient and accurate computational analysis of RNA sequences is becoming increasingly important. Stochastic context-free grammars (SCFGs) are used as a popular tool to model RNA secondary structures. However, algorithms for aligning a RNA sequence to a SCFG are highly compute-intensive. This has so far limited applications of SCFGs to relatively small problem sizes. In this paper we present the design of a parallel RNA sequence-structure alignment algorithm. Its implementation on parallel systems leads to significant runtime savings. This makes it possible to compute sequence-structure alignments of even the largest RNAs such as small subunit ribosomal rRNAs and long subunit ribosomal rRNAs in reasonable time. Copyright (c) 2005 John Wiley & Sons, Ltd. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1002/cpe.952 | CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE |
Keywords | DocType | Volume |
RNA secondary structure, stochastic context-free grammars, parallel processing | Journal | 17 |
Issue | ISSN | Citations |
14 | 1532-0626 | 5 |
PageRank | References | Authors |
0.58 | 4 | 2 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Tong Liu | 1 | 47 | 12.77 |
| Bertil Schmidt | 2 | 363 | 25.65 |