Difference between revisions of "Trinotate"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 21: | Line 21: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 46: | Line 35: | ||
*signalP v4 | *signalP v4 | ||
| − | |||
*RNAMMER | *RNAMMER | ||
Latest revision as of 20:29, 7 December 2023
Description
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/Uniref90), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain 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.
Environment Modules
Run module spider trinotate to find out what environment modules are available for this application.
System Variables
- HPC_TRINOTATE_DIR - installation directory
Additional Information
Additional software included in this module:
- signalP v4
- RNAMMER