miRNA sequence and annotation resources

miRBase

Additional Info

  • Activitiy Active
  • Description
    miRBase is the primary online repository for all microRNA nomenclature, sequences and annotation. This database provides genomic location of miRNAs, miRNA clusters and search or BLAST for precursor and mature miRNA sequences. miRBase mapped reads from short RNA deep-sequencing experiments to microRNAs and users can view these mappings.
  • Main feature miRNA sequences and annotations
  • Unique features
    Stem loop structure and deep sequencing
    Search miRNAs by genomic location
    Search of miRNA clusters
    Search of homolog miRNAs in other species
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category miRNA sequences and annotations
  • Last observe Saturday, 03 September 2016
  • Year published 2004
  • Citations per year 386
  • Last update Sunday, 01 June 2014
  • Updated over past 3 years Yes
  • Relative Popularity 212464

CoGemiR

Additional Info

  • Activitiy Active
  • Description
    CoGemiR purpose to offer an overview of the genomic organization of microRNAs and of its extent of conservation during evolution. The database collects information on genomic location, conservation and expression data of both known and newly predicted microRNAs and displays the data by benefitting a comparative point of view. The database includes a microRNA prediction pipeline to annotate microRNAs in recently sequenced genomes.
  • Main feature Comparative genomic analysis of miRNAs
  • Unique features
    Pre-miRNA and mature sequence
    Expression data in different tissues
    Tissue specificity
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA sequence and annotation
  • Last observe Saturday, 03 September 2016
  • Year published 2008
  • Citations per year 2.375
  • Last update Monday, 06 October 2008
  • Updated over past 3 years No
  • Relative Popularity 1134849

microRNAviewer

Additional Info

  • Activitiy Active
  • Description
    The microRNAviewer web-server includes all known miRNAs of currently fully annotated animal genomes in a visual ‘birds-eye’ view representation. microRNAviewer provides a graphical outlook of the current miRNA world together with sequence alignments and secondary structures of each miRNA.
  • Main feature Conservation of miRNAs in species
  • Unique features
    miRNA alignment and finding mismatches
    miRNA genomic location
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category miRNA sequence and annotation
  • Last observe Saturday, 03 September 2016
  • Year published 2012
  • Citations per year 5.25
  • Last update Tuesday, 28 February 2012
  • Updated over past 3 years No
  • Relative Popularity 757

mirNEST 2.0

Additional Info

  • Activitiy Active
  • Description
    miRNEST 2.0, a comprehensive database of animal, plant and virus microRNAs which is complemented with our extensive miRNA predictions from deep sequencing libraries, data from plant degradome analyses, results of premiRNA classification with HuntMi and miRNA splice sites information.
  • Main feature miRNA sequence with integrative approach
  • Unique features

    Collection of animal, plant and virus microRNAs
    miRNA prediction based on EST data
    Integration with 13 resources include miRNA expression, polymorphisms and targets

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category miRNA sequence and annotation
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 5.75
  • Last update Friday, 15 November 2013
  • Updated over past 3 years Yes
  • Relative Popularity 37939

miROrtho

Additional Info

  • Activitiy Active
  • Description
    The miROrtho database presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. This database was designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data.
  • Main feature Conservation of miRNAs in species
  • Unique features

    Genomic location both known and predicted miRNAs
    Ortholog multiple alignments
    RNA secondary structure conservation

  • Organism Human
  • Category miRNA sequence and annotation
  • Other covered categories

    miRNA expression

  • Last observe Wednesday, 31 August 2016
  • Year published 2009
  • Citations per year 5.86
  • Last update Thursday, 01 January 2009
  • Updated over past 3 years No
  • Relative Popularity 22680

mirvar

Additional Info

  • Activitiy Active
  • Description
    miRvar have comprehensively curated genetic variations in miRNA loci in the human genome and established a computational pipeline to assess potential functional consequences of these variants along with methods for systematic curation and reporting of variations in these loci.
  • Main feature Genetic variations in microRNAs
  • Unique features

    Genetic variants of miRNAs and its functional results

  • Organism Human
  • Category miRNA sequence and annotation
  • Last observe Monday, 29 August 2016
  • Year published 2011
  • Citations per year 3.8
  • Last update Wednesday, 01 June 2011
  • Updated over past 3 years No
  • Relative Popularity 541876

miRiadne

Additional Info

  • Activitiy Active
  • Description
    miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 25 common profiling platforms from nine brands that manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities.
  • Main feature miRNA annotation
  • Unique features

    A tool for re-annotating miRNA name lists or datasets

  • Organism Human
  • Category miRNA sequence and annotation
  • Last observe Saturday, 03 September 2016
  • Year published 2015
  • Citations per year 0
  • Last update Wednesday, 01 July 2015
  • Updated over past 3 years Yes
  • Relative Popularity 0

miRNAfe

Additional Info

  • Activitiy Active
  • Description
    miRNAfe is a comprehensive tool to extract features from RNA sequences. The user only needs to load a file containing the input sequences and select the features to extract and obtains a text file with the features extracted, which can be used to analyze the sequences or as input to a miRNA prediction software. The tool can calculate up to 80 features which have been divided into six pre-defined groups.
  • Main feature RNA sequences features
  • Unique features

    A tool for RNA sequences features extraction

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category miRNA sequence and annotation
  • Last observe Friday, 02 September 2016
  • Year published 2015
  • Citations per year 1
  • Last update Tuesday, 01 December 2015
  • Updated over past 3 years Yes
  • Relative Popularity 60407

mirPub

Additional Info

  • Activitiy Active
  • Description
    mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. This database includes a visualization service that illustrates the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues.
  • Main feature Search for publications related to microRNAs
  • Unique features

    Information about the correlation of microRNAs to any diseases, tissues and genes

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat, Bacteria
  • Category miRNA sequence and annotation
  • Last observe Wednesday, 31 August 2016
  • Year published 2015
  • Citations per year 2
  • Last update Friday, 01 May 2015
  • Updated over past 3 years Yes
  • Relative Popularity 576459

miTRATA

Additional Info

  • Activitiy Active
  • Description
    miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes version 21 miRBase and its strengths lie in biologist-focused web interface, improved scalability via parallel processing and uniqueness as a web tool to perform microRNA truncation and tailing analysis.
  • Main feature 3′ modifications of microRNAs
  • Unique features

    Analysis of 3′ modifications of microRNAs
    Including the loss or gain of nucleotides relative to the canonical sequence

  • Organism Plants
  • Category miRNA sequence and annotation
  • Last observe Monday, 29 August 2016
  • Year published 2015
  • Citations per year 1
  • Last update Saturday, 10 October 2015
  • Updated over past 3 years Yes
  • Relative Popularity 1358300

PNRD

Additional Info

  • Activitiy Active
  • Description
    PNRD plant ncRNA database provide a way to do fundamental research on plant ncRNAs. Specifications in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.
  • Main feature miRNA and ncRNA basic information
  • Unique features

    Including literature mining, experimental targets, predicted targets
    miRNA-ncRNA interaction and miRNA expression

  • Organism Plants
  • Category miRNA sequence and annotation
  • Last observe Thursday, 01 September 2016
  • Year published 2015
  • Citations per year 15
  • Last update Monday, 02 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 41985

VIRmiRNA

Additional Info

  • Activitiy Active
  • Description
    VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. It includes VIRMIRTAR viral miRNA target genes and AVIRMIR antiviral miRNAs encoded by the host against viruses. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics.
  • Main feature Experimentally validated viral miRNAs
  • Unique features

    Including VIRmiRNA, VIRmiRtar and AVIRmir subdatabases
    VIRmiRNA includes 1308 experimentally validated miRNA sequences
    with their isomiRs encoded by 44 viruses in viral miRNA

  • Organism Viruses
  • Category miRNA sequence and annotation
  • Other covered categories
    Single resource target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2014
  • Citations per year 2
  • Last update Friday, 07 November 2014
  • Updated over past 3 years Yes
  • Relative Popularity 858702

WMD3

Additional Info

  • Activitiy Active
  • Description
    Artificial microRNAs (amiRNAs) are 21mer small RNAs, which can be genetically engineered and function to specifically silence single or multiple genes of interest in more than 90 plants, according to the previously determined parameters of target gene selection. WMD3 uses your favorite gene(s), which you want to silence, and designs 21mer amiRNA sequences. You will retrieve oligo sequences to express the small RNA from endogenous miRNA precursors.
  • Main feature Automated design of artificial plant microRNA
  • Unique features

    Platform requires only selection of favorite candidates according to a small set of criteria

  • Organism Plants
  • Category miRNA sequence and annotation
  • Last observe Thursday, 01 September 2016
  • Year published 2008
  • Citations per year 37.25
  • Last update Friday, 01 February 2008
  • Updated over past 3 years No
  • Relative Popularity 2160021