OliCheck

OliCheck selects and validates 40–60 mer oligonucleotide probes for DNA microarray experiments to ensure target specificity and optimal thermodynamic properties while minimizing cross-hybridization across multiple genomes and strains.

Key Features:

• Probe Specificity and Thermodynamic Optimization: An algorithm selects 40–60 mer probes based on optimal thermodynamic criteria and high target specificity to reduce non-specific interactions.
• Cross-Genome Analysis: Integrates sequence information from multiple genomes or strains to enhance genome coverage, including conserved regions.
• Positional Information Integration: Incorporates positional data about predicted target–probe binding regions to refine probe selection beyond sequence alone.
• Experimental Validation: Probe selection was experimentally validated using Staphylococcus aureus, producing extensive genome coverage across different strains.

Scientific Applications:

• Comparative Genomics: Enables design of probes across multiple genomes to compare gene presence, conservation, and variation.
• Molecular Epidemiology: Supports strain-level analyses by providing probes that distinguish genomic differences among strains.
• Deletion Mapping: Facilitates mapping of deletion mutations through high-quality probe placement across genomic regions.
• Transcription Profiling: Supports accurate gene expression analysis by minimizing cross-hybridization and optimizing probe thermodynamics.
• Genetic Variation and Pathogenesis Studies: Aids studies of gene expression patterns, genetic variations, and microbial pathogenesis via reliable probe selection.

Methodology:

Filters extensive oligonucleotide libraries using standard thermodynamic criteria, incorporates positional binding information to refine selection, and employs BLAST analysis for validation, yielding over 97% genome coverage in one Staphylococcus aureus strain.