pLannotate

pLannotate annotates engineered plasmids by identifying functional elements, recombinant and synthetic sequences, and resolving annotation inaccuracies from historical reuse of DNA to improve interpretation of plasmid function.

Key Features:

• Filtering algorithm: Prioritizes relevant feature matches, including incomplete fragments critical for plasmid functionality.
• Recombinant DNA detection: Identifies recombinant DNA derived from diverse domains of life.
• Synthetic and engineered element detection: Detects synthetic sequences and engineered gene expression and regulatory elements often overlooked by traditional pipelines.
• Graphical maps: Generates graphical maps representing annotated plasmid constructs.
• Feature provenance explanations: Provides provenance information for each feature prediction.
• Data export: Exports annotated data in multiple formats for integration with bioinformatics tools.

Scientific Applications:

• Plasmid re-annotation: Improves accuracy of plasmid annotations by resolving ambiguities from historical design reuse.
• Synthetic biology and genetic engineering: Supports prediction of experimental outcomes and validation of engineered constructs by identifying functional and regulatory elements.
• Origin and provenance analysis: Traces and explains the provenance of plasmid features, including recombinant sequences from diverse taxa.
• Bioinformatics integration: Provides exported annotation data for downstream analyses in other bioinformatics tools.

Methodology:

Uses extensive databases of genetic parts and proteins and applies sequence comparison and alignment algorithms together with a filtering algorithm that prioritizes relevant matches, including incomplete fragments, to identify recombinant DNA, synthetic sequences, and engineered regulatory or gene expression elements.