TOA

TOA performs taxonomy-oriented functional annotation of genomic and transcriptomic sequences from non-model plant species to assign ontology- and pathway-based annotations by leveraging homology to reference databases.

Key Features:

• Taxonomy-Oriented Approach: Employs a taxonomy-oriented strategy tailored to non-model plants, including gymnosperms and woody species, to improve annotation relevance.
• Database Integration: Integrates PLAZA databases (Dicots PLAZA 4.0, Monocots PLAZA 4.0, Gymno PLAZA 1.0), NCBI RefSeq Plant, NCBI Nucleotide Database (NT), and the non-redundant protein sequence database (NR).
• Functional Information Extraction: Performs homology searches against protein sequences in the integrated databases and outputs annotations from Gene Ontology, InterPro, EC numbers, KEGG pathways, MapMan, and MetaCyc.
• Input Data Types: Annotates genomic and transcriptomic sequences generated by high-throughput sequencing platforms.
• Computational Implementation: Implemented in Python and runnable on Linux/Mac computers, high-performance computing (HPC) systems, and cloud servers.
• Validation and Performance: Validated against plant benchmark datasets and reported comparative improvements in both the number of annotated sequences and annotation accuracy, including for low-quality sequence datasets and non-model plants.

Scientific Applications:

• Functional annotation of non-model plants: Provides ontology- and pathway-based annotations for gymnosperms and other non-model plant species.
• Gene discovery and characterization: Supports identification and functional characterization of genes in species lacking comprehensive reference genomes.
• Comparative genomics and pathway analysis: Enables comparative analyses and pathway reconstruction using mapped GO, InterPro, EC, KEGG, MapMan, and MetaCyc annotations.
• Annotation of sequencing-derived assemblies and transcriptomes: Facilitates annotation of assemblies and transcriptomes produced by high-throughput sequencing for downstream analyses.

Methodology:

TOA applies a taxonomy-oriented strategy, integrates PLAZA (Dicots 4.0, Monocots 4.0, Gymno 1.0), NCBI RefSeq Plant, NT and NR databases, conducts homology searches against protein sequences, and maps extracted functional information to Gene Ontology, InterPro, EC numbers, KEGG pathways, MapMan, and MetaCyc; it is implemented in Python and can run on Linux/Mac, HPC, and cloud systems.