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BIOINF 05-023: Prediction of Structured Non-Coding RNAs in the Genomes of the Nematodes <i>Caenorhabditis elegans</i> and <i>Caenorhabditis briggsae</i>

Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbø, Runsheng Chen, Peter F. Stadler



  • Caenorhabditis elegans ncRNA candidates conserved in C. elegans and C. briggsae with RNAz classification probability p>0.5
    [fasta format] [bed format] [gff format]

    • A short description of file formats
    >id
    NOTE: FASTA files contain sequences of predicted ncRNAs with 10nt flanking regions.

    BED file format:
    chromosome startRegion endRegion id p strand startCandidate endCandidate

    chromosome: chromosome name
    startRegion, endRegion: genomic coordinates of ncRNA candidate region; a region may contain several conserved alignments; for each region a candidate alignment is chosen
    id: internal type of predicted ncRNA
    p: (RNAz classification probability of best window) * 1000
    strand: reading direction of predicted ncRNA
    startCandidate, endCandidate: genomic coordinates of chosen ncRNA candidate
    NOTE: In BED files start coordinates are 0 based and end coordinates are 1 based (as in UCSC browser)!

    GFF file format:
    chromosome RNAz ncRNA startRegion endRegion strand . Annotation

    startRegion, endRegion: genomic coordinates of ncRNA candidate region
    Annotation:
    RNAz-ID
    Genomic_context[ isolated|intronic|5UTR|3UTR|IntUTR ]
    Promoter[ UM1|UM2|UM3 ]
    Deng_05[ ID in Deng et al. 2005 ]
    Wormbook_WS130[ ID in Stricklin et al. 2005 ]
    Homolog[ Cr ]: ncRNA candidate has a homologous ncRNA in C. remanei
    tRNA-Scan[ tRNA type ]
    MiRNA[ filtered(z-score)|Grad_03(ID in Grad et al. 2003) ]
    Histone
    NOTE: A minority of ncRNA candidates annotated as a UTR element are also annotated as intronic or isolated. This occurs when a gene of GeneBounds track comprises several protein coding regions.
    54 ncRNAs are annotated as 5'UTR as well as 3'UTR, which may be regulatory elements for polycistronic transcripts. Such ncRNAs are labeled with 'IntUTR'.