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 align- ing an RNA sequence to an 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 a PC cluster leads to sig- nificant runtime savings. This makes it possible to compute sequence-structure alignments of even the largest RNAs such as SSU rRNAs and LSU rRNAs in reasonable time. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1109/IPDPS.2004.1303207 | IPDPS |
Keywords | Field | DocType |
rna secondary structure,dynamic programming,structure alignment,sequences,computational biology,stochastic context free grammar,context free grammars,databases,genetics,clustering algorithms,rna,macromolecules,dna,proteins,hidden markov models | Stochastic context-free grammar,RNA,Structural alignment,Gene,Context-free grammar,Computer science,Algorithm,Synchronous context-free grammar,DNA,Nucleic acid secondary structure | Conference |
Citations | PageRank | References |
0 | 0.34 | 11 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Tong Liu | 1 | 47 | 12.77 |
| Bertil Schmidt | 2 | 65 | 7.74 |