What it does
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.
Suggested upstream Galaxy tools
Transcripts
- Trinity: iuc/trinity
Peptides
- TransDecoder: iuc/transdecoder
Genes to transcripts map
- Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map
BLASTP: Peptides vs Uniprot.SwissProt
- NCBI BLAST+ blastp: devteam/ncbi_blast_plus
BLASTX: Transcripts vs Uniprot.SwissProt
- NCBI BLAST+ blastx: devteam/ncbi_blast_plus
HMMER hmmscan: Peptides vs PFAM
- HMMER hmmscan: iuc/hmmer_hmmscan
TMHMM on Peptides
- TMHMM 2.0: peterjc/tmhmm_and_signalp
SignalP on Peptides
- SignalP 3.0: peterjc/tmhmm_and_signalp
Output
The output has the following column headers:
| Column | Description |
| 0 | #gene_id |
| 1 | transcript_id |
| 2 | sprot_Top_BLASTX_hit |
| 3 | RNAMMER |
| 4 | prot_id |
| 5 | prot_coords |
| 6 | sprot_Top_BLASTP_hit |
| 7 | custom_pombe_pep_BLASTX |
| 8 | custom_pombe_pep_BLASTP |
| 9 | Pfam |
| 10 | SignalP |
| 11 | TmHMM |
| 12 | eggnog |
| 13 | Kegg |
| 14 | gene_ontology_blast |
| 15 | gene_ontology_pfam |
| 16 | transcript |
| 17 | peptide |