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ICDS database: interrupted CoDing sequences in prokaryotic genomes.

Emmanuel Perrodou1, Caroline Deshayes, Jean Muller

  • 1Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France.

Nucleic Acids Research
|December 31, 2005
PubMed
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A new database identifies Interrupted Coding Sequences (ICDS) in prokaryotes, caused by frameshifts or errors. This resource aids functional characterization and experimental validation of these gene sequence interruptions.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Frameshifts, stop codons, and sequencing errors create Interrupted Coding Sequences (ICDS).
  • ICDS can impede downstream functional characterization, including in silico analysis and proteomics.
  • Accurate identification of ICDS is crucial for genomic and proteomic studies.

Purpose of the Study:

  • To develop and present a comprehensive database of Interrupted Coding Sequences (ICDS).
  • To provide a web-accessible resource for retrieving ICDS information and genomic localization.
  • To offer optimized primers for experimental validation of predicted ICDS.

Main Methods:

  • A similarity-based approach was employed to detect ICDS across 80 complete prokaryotic genomes.
  • A web interface was developed for species browsing and similarity searches of the ICDS database.

Related Experiment Videos

  • Primer design for re-sequencing was implemented to facilitate experimental validation.

    • Main Results:

    • The Interrupted Coding Sequence (ICDS) database contains identified interruptions in 80 prokaryotic genomes.
    • The database provides gene definitions, genomic localization, and surrounding sequences for each ICDS.
    • Validation through benchmark tests, genomic comparisons, and re-sequencing yielded high specificity (95%) and sensitivity (82%).

    Conclusions:

    • The ICDS database is a valuable resource for researchers studying prokaryotic genomes.
    • The developed prediction strategy and primer design enhance the experimental characterization of ICDS.
    • The database will be regularly updated, expanding its utility for ongoing genomic research.