Prodesign

Prodesign generates oligonucleotide probes to detect members of specific gene families in environmental and genomic samples for metagenomics, microbial ecology, and environmental microbiology studies.

Key Features:

• Gene Family-Specific Probe Design: Generates oligonucleotide probes tailored to detect members of specific gene families present in environmental and genomic samples.
• Spaced Seed Hashing Algorithm: Employs a spaced seed hashing algorithm to identify specific and shared sequence motifs for targeted probe generation.
• Dynamic Re-clustering for Enhanced Detection: Re-clusters sequences that share common words into new gene families and generates specific probes for those newly defined families.
• Flexibility and Efficiency: Designs probes for multiple gene families simultaneously across one or more genomes without requiring predefined parameters such as probe length or melting temperature, improving coverage and speed.

Scientific Applications:

• Metagenomics: Enables design of oligonucleotide probes for detecting gene families within metagenomic datasets.
• Microbial ecology: Supports detection and comparison of gene family distributions to study microbial community structure and interactions.
• Environmental microbiology: Facilitates monitoring and detection of target gene families in environmental samples.
• Biodiversity assessment: Assists in assessing gene-level diversity across complex microbial communities.
• Functional analysis of microbial communities: Aids in targeting gene families for functional profiling of microbial assemblages.

Methodology:

Uses spaced seed hashing to identify specific and shared sequence motifs, dynamically re-clusters sequences sharing common words into new gene families, and generates gene family-specific oligonucleotide probes without requiring predefined probe length or melting temperature.