ProkProbePicker (PPP): A fast program to extract 16S rRNA-targeted probes for prokaryotes

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

This paper describes an efficient software tool ProkProbePicker (PPP) for the design of arrays of 16S rRNA-targeted probes that can be used to determine the genetic affinity of unknown bacteria. Unlike most currently available applications that have been developed to design probes for a single species or bacterial grouping, PPP was designed to extract probes for all major groupings in a known phylogenetic tree. Arrays designed by PPP will allow determination of the genetic affinity of an unknown organism relative to the groups included in the array. PPP employs the Karp-Rabin algorithm for string comparisons and the A VL data structure for a balanced binary search and therefore is more efficient than other tools. As an auxiliary part of PPP, the program OrgMap was designed to help analyze hybridization data based on probes designed by PPP. To test the capability of mapping unknown organisms based on PPP-designed probes, we conducted in silico hybridization experiments on two recently identified organisms. The results showed that a PPP designed array could correctly determine the genetic affinity of these organisms to the genus level in one case and the species level in the other. It is concluded that PPP is a useful tool for the design of arrays that can determine genetic affinity of unknown organisms.

Original languageEnglish (US)
Title of host publicationProceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05
Pages41-47
Number of pages7
StatePublished - 2005
Externally publishedYes
Event2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05 - Las Vegas, NV, United States
Duration: Jun 20 2005Jun 23 2005

Other

Other2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05
CountryUnited States
CityLas Vegas, NV
Period6/20/056/23/05

Fingerprint

Probe
Affine transformation
Unknown
Grouping
Binary search
Phylogenetic Tree
Software Tools
Bacteria
Data structures
Data Structures
Genus
Strings
Experiment
Design
Experiments

Keywords

  • 16S rRNA
  • bacterial identification
  • genetic affinity
  • hybridization probes

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Theoretical Computer Science
  • Software

Cite this

Zhu, D., Willson, R. C., Fofanov, Y., & Fox, G. E. (2005). ProkProbePicker (PPP): A fast program to extract 16S rRNA-targeted probes for prokaryotes. In Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05 (pp. 41-47)

ProkProbePicker (PPP) : A fast program to extract 16S rRNA-targeted probes for prokaryotes. / Zhu, Dianhui; Willson, Richard C.; Fofanov, Yuriy; Fox, George E.

Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05. 2005. p. 41-47.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Zhu, D, Willson, RC, Fofanov, Y & Fox, GE 2005, ProkProbePicker (PPP): A fast program to extract 16S rRNA-targeted probes for prokaryotes. in Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05. pp. 41-47, 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05, Las Vegas, NV, United States, 6/20/05.
Zhu D, Willson RC, Fofanov Y, Fox GE. ProkProbePicker (PPP): A fast program to extract 16S rRNA-targeted probes for prokaryotes. In Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05. 2005. p. 41-47
Zhu, Dianhui ; Willson, Richard C. ; Fofanov, Yuriy ; Fox, George E. / ProkProbePicker (PPP) : A fast program to extract 16S rRNA-targeted probes for prokaryotes. Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05. 2005. pp. 41-47
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