The mosquito Anopheles gambiae is widely studied to dissect mechanism of innate immunity in its response to Plasmodium falciparum. RNAi can be used in Anopheles tissue culture as well as in live mosquitoes for in vivo studies, leading to efficient depletion of target mRNAs. We used VectorBase annotations to generate input files for NEXT-RNAi. Specifically we designed long dsRNAs against 62,138 exons annotated for the mosquito genome (exons longer 560 nt were splitted in two sequences, resulting in overall 74,944 input sequences for NEXT-RNAi).
NEXT-RNAi HTML ouputs are available here
Overall 68.855 designs were obtained, covering 95% of the genome. 89.2% of all genes are covered by at least one design that does not show homology of 19 nt or longer to any other gene. 90.1% of all genes are additionally covered by at least one second, independent design.
Input files and settings used
Input FASTA file
- agambiae_exons_split.zip (7.6MB) containing exon target sequences as input file (-i input).
Targetgroup file (tab-delimited)
agambiae_targetgroups.tab (352KB) defining which VectoBase transcripts belong to the same gene (headers Target and TargetGroup) (TARGETGROUPS option
Bowtie database/index for off-target evaluation
Bowtie database/index containing annotated VectorBase 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 Anopheles 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.