From MetaCentrum
Jump to navigation Jump to search


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 (NCBI-BLAST), protein domain identification (HMMER/PFAM), protein signal prediction (singalP/tmHMM), and comparison to currently curated annotation databases (EMBL Uniprot eggNOG/GO Pathways 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.


GPL, see


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of trinotate and load default version of trinotate as

module avail trinotate/ # list available modules
module load trinotate   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail trinotate

and choose explicit version you want to use.
Trinotate -help
signalp -h
TransDecoder.Predict -h
TransDecoder.LongOrfs -h