We evaluated the Ambion (Silencer Select) and Qiagen (human druggable v3.0 and human whole genome supplement v1.0 sets) siRNA libraries containing 64,781 siRNAs and 70,308 siRNAs, respectively. For annotations NCBI RefSeq release 40 was used.
NEXT-RNAi HTML ouputs for the library evaluations are available here:
Input files and settings used
Input FASTA file
The files contain siRNA sequences used as input for NEXT-RNAi (-i input).
Targetgroup file (tab-delimited)
TargetGroups_GeneID.tab (1.3MB) defining which RefSeq transcripts belong to the same gene (headers Target and TargetGroup) (TARGETGROUPS option)
Bowtie database/index for off-target evaluation
Bowtie database/index containing annotated RefSeq transcripts (release 40) for specificity calculations (-d input):
Feature file with UTR and SNP locations
Tab-delimited feature file containing mappings of UTRs and SNPs (from NCBI dbSNP) to chromosomes that is used to calculate UTR and SNP 'contents' (FEATURE option) of designed reagents: Hs_UTR_SNP.tar.gz (484MB)
FASTA file for homology evaluation
Transcriptome FASTA file to evaluate the homology of the designs using Blast (HOMOLOGY and TXNFASTA options):
Bowtie database/index for seed match evaluation
To compute the number of siRNA seed matches (seed complement frequency) a Bowtie database/index containing all annotated 3'-UTR sequences (RefSeq release 40) was generated to be used with the SEEDMATCH option (Hs_3UTR.tar.gz (26MB)).
Start of program
Descriptions for start parameters used are available here.
Descriptions for all options used are available here.