Annotare protocols

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Associated diseases

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Annotare specifications


Unique identifier OMICS_00741
Name Annotare
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Annotare

Annotare in pipelines

PMCID: 5711377
PMID: 29110754
DOI: 10.7554/eLife.29132.031

[…] were performed by the university of michigan dna sequencing core using the illumina hi-seq 2500 platform. all sequences were deposited in the embl-ebi arrayexpress database (rrid:scr_004473) using annotare 2.0 and are cataloged under the accession number e-mtab-5801. transcriptional quantitation analysis was conducted using 64-bit debian linux stable version 7.10 ('wheezy’). pseudoalignment […]

PMCID: 4370217
PMID: 25803487
DOI: 10.7554/eLife.05098.029

[…] (de) was performed by the university of california, san francisco dna sequencing core using the illumina hi-seq platform. all sequences were deposited in the embl-ebi arrayexpress database using annotare 2.0 and are catalogued under the accession number e-mtab-3339 for the hlos and e-mtab-3158 for sc and de. the university of michigan bioinformatics core obtained the reads files […]

PMCID: 4190437
PMID: 25227120
DOI: 10.1186/1471-2164-15-798

[…] 350 million 50-nt reads were generated over the thirty libraries., raw sequence data and protocol details were submitted to the arrayexpress database ( through the annotare 2.0 submission tool. the experiment has been assigned accession number e-mtab-2736., adaptors in color space (5’-330201030313112312-3’) were removed by cutadapt (version 0.9.5), permitting […]

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Annotare in publications

PMCID: 5482461
PMID: 28644855
DOI: 10.1371/journal.pone.0179645

[…] published studies, it is important to use the same type of clinical material and to test and select the best-performing normalization method for data analysis., supporting raw data were submitted to annotare. the data are publicly available from 7/6/2017 under accession e-mtab-5346., micrornas (mirnas) are small non coding rnas (~21 nucleotides) which play an important role […]

PMCID: 5435347
PMID: 28545140
DOI: 10.1371/journal.pone.0177901

[…] zc3h32 might be implicated in basal mrna metabolism, with this role perhaps being taken over by another protein in procyclic forms., sequences from trypanosomes with reduced zc3h32 are available at annotare as e-mtab-4558; the rna immunoprecipitation is e-mtab-5612., organisms in the phylum euglenozoa rely on trans splicing to process mrnas from polycistronically transcribed precursors. […]

PMCID: 5407766
PMID: 28448534
DOI: 10.1371/journal.pone.0176243

[…] enhance mir-21 activity and subsequent carbohydrate metabolism in humans., all files are available through figshare at array data are available through annotare at, the rotation of the earth and associated light / dark cycles are responsible for entrainment of our circadian system, […]

PMCID: 5870697
PMID: 28369191
DOI: 10.1093/bioinformatics/btx143

[…] the analysis pipeline behind the rnaseq-er api offers an important service to researchers performing rna-seq experiments that choose to submit their data to arrayexpress via submission tool: the deposited studies are not only described by rich, ontology-annotated experimental metadata; the associated raw data is also analysed for free, and for qualifying […]

PMCID: 5357668
PMID: 28386458
DOI: 10.1038/cddiscovery.2017.17

[…] distance and complete linkage. bootstrap was used to evaluate dendrogram’s consistency. enrichment analysis was performed in david database (ease score <0.05). data can be accessed through annotare repository (, the graphpad prism 5 software (la jolla, ca, usa) was used for statistical analyses. all comparisons were conducted […]

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Annotare institution(s)
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA

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