Trinotate

Trinotate performs automatic functional annotation of transcriptomes to assign coding regions, identify gene orthologs, and support interpretation of de novo assembled RNA-sequencing data.

Key Features:

• Automatic Functional Annotation: Automates assignment of functional information to transcripts from assembled transcriptomes.
• De Novo Transcriptome Compatibility: Supports annotation of de novo assembled transcriptomes derived from RNA-sequencing of multiple tissues.
• Broad Organism Applicability: Applies to both model and non-model organisms lacking reference genomes.
• Coding Region Prediction: Predicts putative coding regions within transcript sequences.
• Gene Ortholog Identification: Identifies gene orthologs to facilitate comparative and functional inference.
• Expression Analysis: Enables analysis of gene expression levels across tissues or experimental conditions.

Scientific Applications:

• Regenerative Biology (axolotl limb regeneration): Used to assemble and annotate a de novo axolotl transcriptome from RNA-sequencing, achieving near-complete sequence information for 88% of genes and enabling identification of orthologs such as cirbp (cytoprotective) and kazald1 (manipulation disrupted regeneration).

Methodology:

De novo transcriptome assembly from RNA-sequencing across multiple tissues; assignment of functional annotations including prediction of coding regions and identification of gene orthologs; analysis of gene expression levels across tissues or conditions.