EvryRNA : miRNAFold

Ab initio miRNA prediction in genomes

miRNAFold

Tutorial

    • The sequence should be constituted only with the following nucleotides: A, T, C, G, N, a, t, c, g, n.
    • Single sequence mode: One sequence in FASTA file format, the first line of your file must start with ">"
    • Multifasta mode: Input file could be constituted by several sequences in FASTA format
    • The maximal size of the pre-miRNA that miRNAFold can find.
    • This size is limited to 1000 nucleotides.
    • The minimal size of the pre-miRNA secondary structure.
    • The maximal thermodynamic value ?G of the miRNAFold predicted hairpin.
    • miRNAFold calculates and compares lots of values to the specie features (hairpin size, G+C percent, ...).
    • Each feature has a minimal and a maximal threshold.
    • "Percentage of verified features" is the percentage of calculated value between the two thresholds of a specie feature.
  • miRNAFold can be run on all genomes.
  • Available 78 species are:
    • Homo sapiens
    • Acyrthosiphon pisum
    • Aedes aegypti
    • Amborella trichopoda
    • Anolis carolinensis
    • Apis mellifera
    • Arabidopsis lyrata
    • Arabidopsis thaliana
    • Bombyx mori
    • Bos taurus
    • Brachypodium distachyon
    • Branchiostoma belcheri
    • Branchiostoma floridae
    • Brugia malayi
    • Caenorhabditis brenneri
    • Caenorhabditis briggsae
    • Caenorhabditis elegans
    • Caenorhabditis remanei
    • Canis familiaris
    • Capitella teleta
    • Capra hircus
    • Ciona intestinalis
    • Cricetulus griseus
    • Cucumis melo
    • Cyprinus carpio
    • Danio rerio
    • Drosophila melanogaster
    • Drosophila pseudoobscura
    • Drosophila simulans
    • Drosophila virilis
    • Eptesicus fuscus
    • Equus caballus
    • Fugu rubripes
    • Gallus gallus
    • Glycine max
    • Gorilla gorilla
    • Gossypium raimondii
    • Haemonchus contortus
    • Ictalurus punctatus
    • Linum usitatissimum
    • Macaca mulatta
    • Malus domestica
    • Manihot esculenta
    • Medicago truncatula
    • Monodelphis domestica
    • Mus musculus
    • Nematostella vectensis
    • Nicotiana tabacum
    • Ophiophagus hannah
    • Ornithorhynchus anatinus
    • Oryza sativa
    • Oryzias latipes
    • Ovis aries
    • Pan troglodytes
    • Panagrellus redivivus
    • Petromyzon marinus
    • Physcomitrella patens
    • Plutella xylostella
    • Pongo pygmaeus
    • Populus trichocarpa
    • Pristionchus pacificus
    • Prunus persica
    • Rattus norvegicus
    • Salmo salar
    • Schistosoma mansoni
    • Schmidtea mediterranea
    • Solanum tuberosum
    • Sorghum bicolor
    • Strongyloides ratti
    • Sus scrofa
    • Taeniopygia guttata
    • Tetraodon nigroviridis
    • Tribolium castaneum
    • Triticum aestivum
    • Tupaia chinensis
    • Vitis vinifera
    • Xenopus tropicalis
    • Zea mays
  • Press CTRL + D on the waiting page, to access results later.
  • Each hairpins are displayed with the following informations:
    • Start Position
    • End Position
    • Sequence Size
    • Minimum Free Energy
    • Hairpin
    • Sequence
    • Secondary Structure Visualization
  • NB: In multifasta mode, only size and number of hairpins found for each sequence are displayed.
  • This allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant.
    • Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics 31(20):3377-9. 2015. doi:10.1093/bioinformatics/btv372
  • NB: This option isn't available for multifasta mode
  • Two types of result file are available: with or without secondary structure
For any questions, comments or suggestions about miRNAFold, please feel free to contact: fariza.tahi@ibisc.univ-evry.fr