Trinotate: Transcriptome Functional Annotation and Analysis
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.
A proper 'Trinotate and TrinotateWeb' paper will eventually be written. In the meantime, the best reference for Trinotate is this, where we describe the basics and application of the Trinotate annotation to the Axolotl transcriptome:
Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL. A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063. PubMed PMID: 28099853; PubMed Central PMCID: PMC5419050.