Instructions

Mission Statement:

DEQOR analyzes all possible siRNAs (windows) of a given RNA string for silencing and cross silencing potential in RNA interference.

Usage:

Choose a target database and the window size (number of nucleotides per subsequence).
Paste your raw RNA sequence into the text box.
Adjust display filters and/or quality parameters according to your likings.
Press submit. In case of long sequences and a large database the search might take a considerable amount of time!

Functionality:

The overall functionality is twofold: First, the given sequence is checked for cross-silencing small interfering RNAs (siRNAs), i.e. those with homologues elsewhere in the genome/transcriptome. Second, all subsequence windows are tested for their overall quality as silencers: (GC ratio, Poly bp, correct asymmetry of the siRNA)

Sequence Processing

the complete sequence is searched against the chosen target database (NCBI blastn) in order to detect the original gene. If one or more alignments with an E-value less than the selected cutoff (default: 10E-70) are found, subsequence hits against this/these gene(s) are not shown, as all subsequences would match. Afterwards, a blastN-search is performed with all windows of the given size.
all subsequences are analyzed for their sequencing quality according to state-of-the-art criteria: GC - content between 20% and 50%; asymmetry of siRNA; no poly-bp stretches.
the output is filtered against the given display filter criteria and ordered with respect to quality. Cross silenced genes and recognized origins are linked to the ENSEMBL and NCBI databases, respectively.