Trinotate protocols

Trinotate specifications

Information


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
Requirements TransDecoder, sqlite, NCBI BLAST+, HMMER/PFAM Protein Domain Identification
Source code URL https://codeload.github.com/Trinotate/Trinotate/tar.gz/v3.0.2
Maintained Yes

Subtool


  • TrinotateWeb

Versioning


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Trinotate IN pipelines

 (19)
2018
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. 1b). 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 […]

2018
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 v3.0.228; 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 […]

2018
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 (apweiler et al., 2004), identified protein sequence […]

2017
PMCID: 5450047
PMID: 28572841
DOI: 10.1186/s13068-017-0828-7

[…] sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an n50 of 1134 bp. transdecoder and trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to uniprotkb/swiss-prot and uniref90 databases, searching for known transcripts, proteins, protein […]

2017
PMCID: 5471912
PMID: 28615048
DOI: 10.1186/s12864-017-3846-8

[…] populus trichocarpa (9%), glycine max (5%), oryza sativa (5%) and arabidopsis (1.1%) (fig. 2b).fig. 2 , champak unigenes were functionally classified into different gene ontology (go) terms using trinotate [25]. classification showed that 38% of the annotated genes were involved in biological process, 29.5% in cellular component and 32.5% in molecular function (additional file 2). […]

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