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A practical and robust sequence search strategy for structural genomics target selection.

James E Bray1, Russell L Marsden, Stuart C G Rison

  • 1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. james.bray@sgc.ox.ac.uk

Bioinformatics (Oxford, England)
|June 18, 2004
PubMed
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A new strategy prioritizes genes for structural genomics by assessing sequence similarity to known proteins. This adaptable method uses two thresholds and six levels, applicable across various genomes and algorithms.

Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Structural genomic projects require effective strategies to prioritize gene targets based on sequence similarity to known proteins.
  • The increasing availability of protein comparison software necessitates a robust prioritization scheme independent of specific algorithms and adaptable to varying similarity thresholds.

Purpose of the Study:

  • To develop a universal and robust target selection strategy for structural genomics.
  • To create a prioritization scheme that is algorithm-independent and incorporates flexible sequence similarity thresholds.

Main Methods:

  • A novel strategy was developed to assign priority levels to all genes within any given genome.
  • Structural assignments were calculated using two distinct thresholds, resulting in six prioritization levels (1-6) for whole and partial gene regions.

Related Experiment Videos

  • The methodology is designed for implementation with any fold recognition or homology detection algorithms.

    • Main Results:

    • The developed strategy successfully assigns priority levels to all genes across 10 diverse genomes.
    • The prioritization scheme effectively categorizes both whole genes and partial gene regions.
    • The approach demonstrated its versatility by utilizing both SSEARCH and PSI-BLAST programs.

    Conclusions:

    • A robust and universally applicable target selection strategy for structural genomics has been successfully developed.
    • This method provides a flexible framework for prioritizing gene regions based on sequence similarity, adaptable to various genomic datasets and computational tools.
    • The strategy offers a valuable tool for guiding structural genomics efforts efficiently.