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Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
Trinotate includes TrinotateWeb, which provides a locally-driven web-based graphical interface for navigating transcriptome annotations and analyzing transcript expression and differential expression using the Trinity/RSEM/Bioconductor analysis framework.
Visit the outline on the upper right side of this page for documentation on installing and running Trinotate.