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Related Experiment Videos

AMOD: a morpholino oligonucleotide selection tool.

Eric W Klee1, Kyong Jin Shim, Michael A Pickart

  • 1Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary
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AMOD is a web tool for nucleotide sequence analysis and antisense morpholino oligonucleotide design. It aids in functional genomics by identifying target-specific morpholinos for research applications.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Functional evaluation of nucleotide sequences is crucial for genetic research.
  • Antisense morpholino oligonucleotides (morpholinos) are widely used tools in functional genomics.
  • Designing effective and target-specific morpholinos requires sophisticated computational approaches.

Purpose of the Study:

  • To introduce AMOD, a web-based program for the functional evaluation of nucleotide sequences.
  • To facilitate the selection of target-specific antisense morpholino oligonucleotides.
  • To support functional genomics screens by providing a tool for morpholino design.

Main Methods:

  • AMOD analyzes submitted nucleotide sequences using translation initiation site prediction and sequence-to-sequence comparisons.

Related Experiment Videos

  • It computes base composition and homodimerization values for potential morpholinos within defined subsequences.
  • Morpholino candidates are selected based on these properties and compared against genomic and transcriptome databases.

    • Main Results:

    • AMOD characterizes sequence features essential for effective morpholino design.
    • The program identifies target-specific enriched morpholinos by comparing candidates with biological databases.
    • AMOD has been successfully employed to design approximately 200 morpholinos for zebrafish functional genomics screens.

    Conclusions:

    • AMOD provides a valuable computational resource for designing antisense morpholino oligonucleotides.
    • The tool enhances the efficiency and specificity of morpholino selection for functional genomics studies.
    • AMOD is freely accessible, supporting broader research applications in academia and industry.