OligoWiz

OligoWiz designs oligonucleotide probes for DNA microarrays by evaluating sequence annotations and probe-quality parameters to optimize probe placement and specificity.

Key Features:

• Sequence annotation integration: Integrates sequence annotations including exon/intron structures, untranslated regions (UTRs), and transcription start sites to inform probe placement.
• Probe quality parameters: Evaluates cross-hybridization potential, melting temperature (Tm), probe folding, position within the transcript, and low-complexity regions when scoring candidate oligonucleotides.
• Automatic probe placement: Performs automatic placement of multiple probes per transcript to generate probe sets covering transcripts.
• Customizable parameters: Allows addition of custom scores such as homology, DeltaTm, low-complexity filters, position-specific criteria, and GATC-only sequence selection.
• Cross-species transcript detection analysis: Analyzes probe sets for their ability to detect transcripts from multiple organisms for comparative or multi-species studies.

Scientific Applications:

• Gene expression profiling: Selects probes to support consistent hybridization and reliable measurement of transcript abundance on DNA microarrays.
• Transcriptome analysis: Enables position-specific probe placement and multiple probes per transcript for detailed transcriptome interrogation.
• Comparative genomics / multi-species studies: Designs oligonucleotide sets suitable for detecting and comparing transcripts across multiple organisms.

Methodology:

Systematic evaluation of candidate oligonucleotides against predefined quality parameters and integration of sequence annotations to optimize probe placement, with support for adding custom scoring parameters.