Non-coding RNAs in Ciona Intestinalis: Supplemental Material
Non-Coding RNAs in Ciona intestinalis
Kristin Missal,
Dominic Rose,
Peter F. Stadler
Supplemental Material
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/.