All predicted exons (71,788) from the 'official gene set' of the recently sequenced genome of the red flour beetle, Tribolium castaneum, were used to calculate independent designs of long dsRNAs for the Tribolium genome (exons longer 560 nt were additionally splitted in two sequences, resulting in overall 80,671 input sequences). Tribolium has become an important model organism for developmental and evolutionary studies and is suitable for RNAi by injection of long dsRNAs. Information on predicted genes and sequences was obtained from BeetleBase that integrates sequence annotations for Tribolium.
NEXT-RNAi HTML ouputs are available here
Overall 71,293 designs were obtained, covering 99.4% of the genome. 92.9% of all genes are covered by at least one design that does not show homology of 19 nt or longer to any other gene. 83.2% of all genes are additionally covered by at least one second, independent design.
Input files and settings used
Input FASTA file
beetlebase_exons_split.zip (6.6MB) containing exon target sequences as input file (-i input) (parsed from Tribolium GFF files).
Targetgroup file (tab-delimited)
beetlebase_targetgroups.tab (732KB) defining which BeetleBase transcripts belong to the same gene (headers Target and TargetGroup) (TARGETGROUPS option)
Bowtie database/index for off-target evaluation
Bowtie database/index containing annotated BeetleBase transcripts for specificity calculations (-d input):
Bowtie database/index for mapping of reagents
The Bowtie database/index (GENOMEBOWTIE option) for mapping of reagents to the Tribolium genome:
Bowtie indexes for genomes are also available through the Bowtie webpage.
FASTA file for homology evaluation
Transcriptome FASTA file to evaluate the homology of the designs using Blast (HOMOLOGY option):
Start of program
Descriptions for start parameters used are available here.
Descriptions for all options used are available here.