Annocript

Annocript annotates de novo eukaryotic transcriptomes to identify protein-coding transcripts, predict putative long non-coding RNAs (lncRNAs), and assign functional annotations such as Gene Ontology, UniPathways and Enzyme Commission (EC) numbers.

Key Features:

• Dual annotation capability: Combines annotation of protein-coding transcripts with prediction of putative lncRNAs within whole transcriptomes.
• BLAST analysis against UniProt: Performs BLAST searches of transcripts against the UniProt database to identify protein-coding genes.
• Conserved domain and nucleotide analysis: Integrates the NCBI Conserved Domain Database and nucleotide divisions for domain-specific and nucleotide-level annotation.
• Gene Ontology integration: Maps annotated transcripts to Gene Ontology (GO) terms for functional characterization.
• Pathway and enzyme annotation: Assigns UniPathways mappings and Enzyme Commission (EC) numbers to support pathway and enzyme classification.
• Summary statistics generation: Produces summary statistics for annotated transcriptomes to provide overview metrics of the analysis.

Scientific Applications:

• Transcriptome research: Enables comprehensive annotation of coding and non-coding RNAs in de novo eukaryotic transcriptomes.
• Functional genomics: Supports inference of gene functions and biological processes via GO, pathway and EC annotations.
• Comparative genomics: Facilitates cross-species or condition-based comparisons by providing standardized annotations across transcriptomes.

Methodology:

Automates downloading, indexing and analysis of required databases, executes BLAST searches (e.g., against UniProt), integrates annotations from the NCBI Conserved Domain Database, nucleotide divisions, Gene Ontology, UniPathways and EC numbers, and generates summary statistics for large de novo transcriptome datasets.