A parallel computing algorithm for 16S rRNA probe design

Dianhui Zhu, Yuriy Fofanov, Richard C. Willson, George E. Fox

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

With the continuing rapid increase in the number of available 16S ribosomal RNA (rRNA) sequences, it is a significant computational challenge to efficiently design 16S rRNA targeted probes. In our previous work, we designed a fast software tool called ProkProbePicker (PPP) that takes O (log N) time for a worst-case scenario search. Despite this improvement, it can still take many hours for PPP to extract probes for all the clusters in a phylogenetic tree. Herein, a parallelized version of PPP is described. When run on 80 processors, this version of PPP took only 67 min to extract probes, while some 87 h were needed by the sequential version of PPP. The speedup increased linearly with the increase of CPU numbers, which revealed the outstanding scalability of the parallelized version of PPP.

Original languageEnglish (US)
Pages (from-to)1546-1551
Number of pages6
JournalJournal of Parallel and Distributed Computing
Volume66
Issue number12
DOIs
StatePublished - Dec 2006
Externally publishedYes

Fingerprint

Parallel processing systems
Parallel Computing
Probe
Phylogenetic Tree
Software Tools
Program processors
Scalability
Speedup
Linearly
Scenarios
Design
Ribosomal RNA

Keywords

  • 16S rRNA targeted probes
  • Genetic affinity
  • Parallel algorithm

ASJC Scopus subject areas

  • Computer Science Applications
  • Hardware and Architecture
  • Control and Systems Engineering

Cite this

A parallel computing algorithm for 16S rRNA probe design. / Zhu, Dianhui; Fofanov, Yuriy; Willson, Richard C.; Fox, George E.

In: Journal of Parallel and Distributed Computing, Vol. 66, No. 12, 12.2006, p. 1546-1551.

Research output: Contribution to journalArticle

Zhu, Dianhui ; Fofanov, Yuriy ; Willson, Richard C. ; Fox, George E. / A parallel computing algorithm for 16S rRNA probe design. In: Journal of Parallel and Distributed Computing. 2006 ; Vol. 66, No. 12. pp. 1546-1551.
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