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Database Commons - miROrtho

miROrtho

Citations: 55

z-index 6.11

Short name miROrtho
Full name The catalogue of animal microRNA genes
Description miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine.
URL http://cegg.unige.ch/mirortho
Year founded 2007
Last update & version 2008-10-15    v1.0
Availability Free to all users
University/Institution hosted University of Geneva
Address 1211 Geneva, Switzerland
City Geneva
Province/State
Country/Region Switzerland
Contact name Evgeny M. Zdobnov
Contact email evgeny.zdobnov@unige.ch
Data type(s)
Major organism(s)
Keyword(s)
  • miRNA
Publication(s)
  • miROrtho: computational survey of microRNA genes. [PMID: 18927110]

    Daniel Gerlach, Evgenia V Kriventseva, Nazim Rahman, Charles E Vejnar, Evgeny M Zdobnov
    Nucleic acids research 2009:37(Database issue)
    55 Citations (Google Scholar as of 2016-06-09)

    Abstract: MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We 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. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support.

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Accessibility

Rate of accessibility:
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200 OK2018-01-09
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200 OK2017-12-26
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200 OK2017-11-28
200 OK2017-11-24
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200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
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200 OK2017-09-22
200 OK2017-09-19
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200 OK2017-09-08
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200 OK2017-09-01
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200 OK2017-08-22
200 OK2017-08-18
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200 OK2017-03-14
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200 OK2017-03-07
200 OK2017-03-03
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200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
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200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
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200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
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200 OK2016-10-04
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200 OK2016-09-09
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200 OK2016-07-08
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200 OK2016-06-14
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200 OK2016-06-07
200 OK2016-06-03
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200 OK2016-05-27
200 OK2016-05-24
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200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
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200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
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200 OK2016-01-04

Tags

RNA Standard, Ontology and Nomenclature
Drosophila melanogaster Homo sapiens Mus musculus
miRNA

Record metadata

  • Created on: 2015-07-21
  • Curated by:
    • Zhang Zhang [2016-04-26]
    • Lin Liu [2016-03-30]
    • Mengwei Li [2016-02-20]
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