Transcriptator

Transcriptator performs functional annotation of differentially expressed transcripts and conducts Gene Ontology enrichment and GO-Slim analyses while predicting non-coding RNAs to support transcriptome characterization in organisms lacking a reference genome.

Key Features:

• Functional annotation and GO enrichment: Uses BLAST (Basic Local Alignment Search Tool) and DAVID web services to assign functional annotations and perform GO enrichment analyses.
• Integration with QuickGO: Queries QuickGO web services to retrieve GO terms and perform GO-Slim analysis for high-level GO categorization.
• Non-coding RNA prediction: Integrates PORTRAIT for ab initio prediction of transcriptomic non-coding RNAs.
• Enrichment of pathways, domains and interactions: Identifies enriched pathways, protein domains, gene/protein features, and protein-protein interactions from annotation data.
• Data clustering and tabular reporting: Clusters transcripts based on functional annotations and generates detailed per-transcript tabular reports containing functional and GO annotations.
• Support for NGS and micro-array datasets: Processes de novo assembled reads and expression profiles from Next-Generation Sequencing (NGS) and micro-array experiments, including differentially expressed transcripts.
• Modular architecture: Employs a modular design that permits addition of plugins to extend analysis capabilities.

Scientific Applications:

• Annotation of non-referenced organisms: Characterizes de novo assembled transcriptomes from organisms lacking a reference genome.
• Functional interpretation of differential expression: Identifies enriched GO terms, pathways, domains, and interactions from RNA-seq and micro-array differential expression studies.
• Non-coding RNA discovery and regulatory inference: Predicts non-coding RNAs and supports investigation of their potential regulatory roles in transcriptomic datasets.

Methodology:

Performs BLAST searches and queries QuickGO and DAVID web services for GO, GO-Slim, pathway, domain and interaction annotations, uses PORTRAIT for ab initio non-coding RNA prediction, clusters transcripts by functional annotations, and generates per-transcript tabular reports and GO enrichment results.