CATO

CATO performs clone sequence alignment, comparison, evaluation, and selection to process and prioritize candidate clones from high-throughput cloning datasets.

Key Features:

• Integrated Workflow: Consolidates alignment, comparison with reference sequences, editing, and organization of clone sequences into a single processing workflow.
• Standard Data Format Compatibility: Handles input and output in standard data formats to integrate with existing clone processing pipelines and other bioinformatics tools.
• Sequence Alignment and Visualization: Employs an alignment algorithm to match candidate sequences against reference sequences and provides multi-level visualizations including a top-level summary of best-matching candidates, nucleotide-level alignments against a single reference, and pair-wise alignment views.
• Customizable Matching Criteria: Implements customizable minimum matching thresholds for clone validation.
• Editable Reference Sequences: Allows editing and swapping of reference sequences within the processing workflow.
• Export and Reporting: Exports results into summary files for documentation and downstream analysis.

Scientific Applications:

• High-throughput cloning: Processes and ranks large volumes of clone sequences for projects that generate substantial sequencing output.
• Clone validation and selection: Validates candidate clones by comparing sequences to references and applying defined matching criteria to select optimal clones.
• Sequence accuracy assessment and workflow optimization: Facilitates assessment of nucleotide-level sequence accuracy and supports optimization of cloning workflows through prioritized selection and reporting.

Methodology:

Matches candidate sequences against reference sequences using an alignment algorithm, generates nucleotide-level and pair-wise alignments for visualization, applies user-defined matching thresholds for validation, supports editing/swapping reference sequences, and exports results into summary files.