Probe Select

Probe Select optimizes the selection of oligonucleotide probes for high-density DNA microarrays by combining sequence information and hybridization free energy calculations to choose probes that minimize background hybridization.

Key Features:

• Algorithmic optimization: Integrates sequence data with hybridization free energy metrics to predict and enhance oligo performance on microarrays.
• Heuristic selection: Employs an efficiently computable heuristic that approximates the true optimum probe set across large genomic scales.
• Probe length options: Selects short (20–25 bases) or long (50 or 70 bases) oligonucleotides from genes or open reading frames (ORFs).
• Background hybridization minimization: Prioritizes probes that reduce nonspecific hybridization to improve accuracy of gene expression measurements.
• Cost optimization: Reduces the number of probes required per gene, enabling more genes to be assayed per microarray and lowering production cost.
• Genome-wide scalability: Applied to complete genomes of multiple model organisms, demonstrating scalability and robustness.

Scientific Applications:

• Microarray probe design: Designing optimal oligos for high-density DNA microarrays to improve gene expression profiling accuracy.
• Genome-wide probe selection: Generating probe sets across entire genomes for comparative and functional genomics studies.
• ORF-targeted assays: Selecting probes specifically from genes or open reading frames for targeted expression analysis.

Methodology:

Uses sequence-based scoring and hybridization free energy calculations together with an efficiently computable heuristic to select short (20–25 bases) or long (50 or 70 bases) oligos from genes/ORFs for genome-wide probe optimization.