Additional file 4.
Detailed output for a long dsRNA that targets the Drosophila gene csw (FBgn0000382). The box 'dsRNA information' provides information about the primers (for example, sequence, melting temperature, GC content) required for the synthesis. 'Primer pair penalty' is an overall quality score for the primer pair. The lower this score is, the higher is the predicted quality of the primer pair. Further, the full amplicon sequence, its length and location in the genome (in the format chromosome:start..end(orientation)) are presented. The 'Target information' box shows the intended target(s) and transcript(s) as well as other (unintended) targets and transcripts ('NA' means that no target was found). The intended transcripts are those with most siRNA hits (here, all 203 19-nucleotide siRNAs target the 4 isoforms of csw). The intended gene is then defined over the intended transcripts. The 'Reagent quality' box shows the overall number of siRNAs (here 19-nucleotide siRNAs) contained within the long dsRNA sequence, the number of siRNAs that are 'On-target' (the intended target) and those that are 'Off-target' or have 'No-target'. Further quality features computed for this run were the number of conserved miRNA seeds ('mirSeed') in this dsRNA, the number of 'Efficient siRNAs' (here equal to the overall number of siRNAs, since the efficiency cutoff was set to 0), the 'Average efficiency score' (mean efficiency score of all siRNAs contained in the long dsRNA), and the number of 'Low complexity regions' and 'CAN' repeats contained in the long dsRNA. Additionally, the overlap to UTRs (this long dsRNA completely overlaps with annotated UTRs) and the sequence homology to all transcripts (here only to the intended target) were analyzed in this run. The 'Genome Browser' box visualizes the long dsRNA in its genomic context.
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Horn et al. Genome Biology 2010 11:R61 doi:10.1186/gb-2010-11-6-r61