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Trinotate (version 3.2.2+galaxy0)
Trinity output: Assembled Transcripts
Transdecoder output: transdecoder_pep
Genes to transcripts map output. Containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity
[optional] NCBI BLAST+ blastp output. Output format: Tabular (standard 12 columns)
[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)
[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)
Report options
Report options 0
Can be used for visualization purpose

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



Genes to transcripts map

BLASTP: Peptides vs Uniprot.SwissProt

BLASTX: Transcripts vs Uniprot.SwissProt

HMMER hmmscan: Peptides vs PFAM

TMHMM on Peptides

SignalP on Peptides


The output has the following column headers:

Column Description
0 #gene_id
1 transcript_id
2 sprot_Top_BLASTX_hit
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