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Related Experiment Videos

Graphical representation of ribosomal RNA probe accessibility data using ARB software package.

Yadhu Kumar1, Ralf Westram, Sebastian Behrens

  • 1Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany. yadhu@mikro.biologie.tu-muenchen.de

BMC Bioinformatics
|March 22, 2005
PubMed
Summary

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Designing effective microbial identification probes is crucial. The ARB software

Area of Science:

  • Microbiology
  • Bioinformatics

Background:

  • Hybridization probes are standard for microbial identification and community analysis.
  • Fluorescence in situ hybridization (FISH) enables single cell identification and localization.
  • In silico design and evaluation of oligonucleotide probes are critical for successful experiments.

Purpose of the Study:

  • To introduce enhanced probe design and evaluation tools within the ARB software package.
  • To improve the accuracy and success rate of in situ hybridization experiments through better probe design.

Main Methods:

  • Utilizing the PROBE Design tools in the ARB software package for oligonucleotide probe design.
  • Incorporating criteria such as diagnostic sequence differences, higher-order structure, conservation, and target accessibility.

Related Experiment Videos

  • Employing new visualization tools for examining sequence-associated information (SAI) with user-defined colors.

    • Main Results:

    • The ARB software's PROBE Design tools consider multiple criteria for probe design.
    • New visualization tools allow detailed examination of sequence-associated information, including higher-order structure and in situ accessibility.
    • Sequence-associated information can be visualized within ARB editors and the PROBE Match tool.

    Conclusions:

    • The ARB software facilitates in silico probe design and evaluation considering in situ accessibility.
    • Evaluating probe targets against higher-order rRNA structure is vital for successful in situ hybridization.
    • The ARB software package and probe accessibility data are publicly available.