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BIOINF 05-008: Non-coding RNAs in <i>Ciona intestinalis</i>

Kristin Missal, Dominic Rose, Peter F. Stadler


  • Ciona intestinalis ncRNA candidates conserved in C. intestinalis and C. savignyi with RNAz classification probability p>0.5
    [fasta format] [bed format]
  • Ciona intestinalis ncRNA candidates conserved in C. intestinalis, C. savignyi and O. dioica with RNAz classification probability p>0.5
    [fasta format] [bed format]
  • List of Ciona intestinalis ncRNA candidates with identified homologs [bed format]
  • List of Ciona intestinalis miRNA predictions [fasta format] [bed format]

    • A short description of file formats

    FASTA-header:

    >id scaffold startDB endDB p strand startSeq endSeq

    id: internal type of predicted ncRNA
    scaffold: scaffold name
    startDB, endDB: genomic coordinates of predicted ncRNA (assembly JGI v.1.0*)
    p: RNAz classification probability
    strand: reading direction of predicted ncRNA
    startSeq, endSeq: genomic coordinates of predicted ncRNA with 10nt flanking region

    NOTE: In FASTA files start coordinates and end coordinates are 1 based!
    FASTA files contain sequences of predicted ncRNAs with 10nt flanking regions.


    BED file format:

    scaffold startDB endDB [id|annotation] p strand

    scaffold: scaffold name
    startDB, endDB: genomic coordinates of predicted ncRNA (assembly JGI v.1.0*)
    id: internal type of predicted ncRNA
    annotation: type of identified homologous known ncRNA
    p: (RNAz classification probability) * 1000
    strand: reading direction of predicted ncRNA

    NOTE: In BED files start coordinates are 0 based and end coordinates are 1 based (as in UCSC browser)!





    *These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/.