Trinotate protocols

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Trinotate specifications


Unique identifier OMICS_19343
Name Trinotate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0.2
Stability Stable
TransDecoder, sqlite, NCBI BLAST+, HMMER/PFAM Protein Domain Identification
Source code URL
Maintained Yes


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Trinotate in pipelines

PMCID: 5771010
PMID: 29338737
DOI: 10.1186/s12985-018-0926-6

[…] the presence of highly conserved genes with 2748 core proteins from conserved regions of eukaryotes. transdecoder was used to identify the candidate coding regions within transcript sequences, and trinotate was used for performing the functional annotation of unigenes and orfs., the clean reads from viruliferous and nonviruliferous guts were separately mapped back to the assembled unigenes. […]

PMCID: 5771010
PMID: 29338737
DOI: 10.1186/s12985-018-0926-6

[…] ranged from 297 bp to 15,858 bp, with a mean length of 1049 and an n50 of 1491 (fig. ). to annotate the unigenes, we searched reference sequences against nt, nr, pfam and uniprot databases, using trinotate and blast with a cut-off e-value of 10− 5. 21,259 (38.57%) unigenes were annotated at least in one database, including 6623 in nt, 18,556 in nr, 12,457 in blastp and 17,772 in blastx […]

PMCID: 5799185
PMID: 29402916
DOI: 10.1038/s41598-018-20744-z

[…] transcripts were differentially expressed between pregnant and non-pregnant animals (fdr-adjusted p < 0.001). approximately 43% of these differentially regulated transcripts were annotated by trinotate v3.0.2; on the basis of similarity to known genes in the pfam (v31.0) and swissprot (release 2017_2) databases. pearson correlation and principal component analyses of gene expression data […]

PMCID: 5809607
PMID: 29434336
DOI: 10.1038/s41598-018-21268-2

[…] showed that 39,579 and 33,510 transcripts were expressed in the roots and leaves, respectively (displayed in fig. ). the function of each unigene set in c. hupingshanensis was then annotated by trinotate (version r20131110) based on homologies to putative or known sequences available in public databases (table ). in addition, a gene ontology (go) analysis, which is a major bioinformatic […]

PMCID: 5816582
PMID: 29473008
DOI: 10.7717/peerj.4394

[…] using a bonferroni correction to account false discovery across multiple tests. all analyses were performed using r (version 3.3.2)., the functional annotation of transcripts was based on the trinotate pipeline (version 3.0.1). we matched microarray probe sequences to known sequences using blast against the swissprot annotated database (), identified protein sequence homology using hmmer […]

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Trinotate in publications

PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] transmembrane helices (tmhmm) and signal peptide cleavage sites (signalp). all the outputs from blastx, blastp, hmmer/pfam, tmhmm, and signalp were combined into a single annotation file using trinotate (suppl. figure  and table ). this assembly resulted in 9,695 transcripts with predicted pfam domains, 6,167 transcripts with predicted transmembrane helices, 1,099 transcripts with a signal […]

PMCID: 5945926
PMID: 29780371
DOI: 10.3389/fmicb.2018.00859

[…] the suppressive and non-suppressive fields (12 samples) are deposited in the ncbi short read archive (study srp126206; accession numbers srr6349879–srr6349890). the assembled metatranscriptome and trinotate annotation file is available through figshare (doi:10.6084/m9.figshare.5657215)., the raw illumina paired-end sequence reads were quality filtered with the adaptors and low quality bases […]

PMCID: 5902700
PMID: 29692800
DOI: 10.3389/fgene.2018.00120

[…] than 95% similarity and low complexity sequences, respectively. the transdecoder package ( was used to identify the contigs candidate coding regions. meanwhile, trinotate pipeline ( was employed for annotation of the sequences through the following databases: uniprot (uniref90 + swissprot) with cut-off value of 1e10−5, gene […]

PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] final set of gene models. although braker1 has been shown to perform equally well with masked and unmasked genome sequence, we used the soft masked genome to prevent any corrupt gene predictions (). trinotate version 3.0.2 ( and interproscan version 5.21-60.0 () were used to functionally annotate the predicted gene models. transcript sequences in fasta format […]

PMCID: 5869700
PMID: 29588496
DOI: 10.1038/s41598-018-23667-x

[…] differential gene expression data and the assembled transcriptome are submitted to array express under accession number e-mtab-6388., genes within the assembled transcriptome were annotated using trinotate. putative gene functions were identified by gene ontology (go) analysis. of the 221,659 trinity genes 37,895 were assigned minimum one gene ontology (go)-term. go mapping resulted in 62 go […]

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