chipD

chipD generates DNA oligonucleotide probe designs for high-density tiling arrays to support applications such as Chromatin Immunoprecipitation on chip (ChIP-chip) and gene-expression profiling.

Key Features:

• Probe selection algorithm: Implements an advanced probe selection algorithm that accepts target sequences and customizable design parameters.
• Specificity optimization: Optimizes probes to uniquely bind intended targets and minimize cross-hybridization.
• Thermodynamic consistency: Selects probes with similar thermodynamic properties to promote uniform hybridization conditions.
• Homogeneous target coverage: Achieves even probe coverage across target sequences to minimize gaps.
• Output reporting: Produces text-format output listing each probe's sequence, genomic location, targeted strand, and hybridization characteristics.
• High-density tiling array design: Targets design specifically for high-density tiling arrays used in genomic assays.

Scientific Applications:

• ChIP-chip: Designing tiling arrays for Chromatin Immunoprecipitation on chip experiments.
• Gene-expression profiling: Designing tiling arrays for gene-expression profiling studies.
• Microarray tiling for bacterial and yeast genomes: Generating probe sets for tiling arrays applied to bacterial and yeast genomes.

Methodology:

The probe selection algorithm optimizes probes for specificity, thermodynamic consistency, and homogeneous target coverage from user-provided target sequences and parameters, producing text output with probe sequence, genomic location, strand, and hybridization characteristics.