Chorus2

Chorus2 enables genome-scale design and optimization of single-copy oligonucleotide-based probes for fluorescence in situ hybridization (FISH) to support molecular cytogenetics and comparative genomic studies.

Key Features:

• Genome-scale probe design: Generates genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (FISH).
• Single-copy oligonucleotide selection: Selects single-copy oligonucleotides to increase probe specificity.
• Repetitive element removal: Eliminates repetitive elements during oligo selection to improve specificity, with reported superior repeat removal compared to Chorus and OligoMiner.
• Cross-species conservation analysis: Identifies oligos conserved among related species to enable cross-species probe design.
• Support for unassembled genomes: Enables development of FISH probes from plant species lacking assembled genomes.
• Optimization of selection: Optimizes selection parameters to enhance the efficiency and accuracy of probe design.

Scientific Applications:

• Plant molecular cytogenetics: Designing genome-scale FISH probes for molecular cytogenetics studies in plants.
• Comparative and evolutionary studies: Generating conserved probes for comparative studies and evolutionary research among phylogenetically related plant species.
• Probes from unassembled genomes: Developing FISH probes for plant species that lack assembled genomes.
• Non-plant and mammalian research: Applying FISH probe design approaches to mammalian and other non-plant species for molecular cytogenetics analyses.

Methodology:

Computational steps explicitly include selection of single-copy oligonucleotides, removal of repetitive elements, identification of oligos conserved among related species, development of probes from unassembled genomes, and optimization of selection parameters for improved efficiency and accuracy.