Scrambler is an accompanying tool to MASON which can be used to generate scrambled control sequences for ASOs. The algorithm takes in an ASO sequence of 7-15 nucleotides and generates scrambled sequences by shuffling the sequence while keeping the nucleotide content constant. Similar to the MASON algorithm, it then screens for off-targets and evaluates which sequences can serve as good scrambled controls.
Please select a unique custom ID to store the result
Select one of the preset genomes or use "Own files" to upload your own genome.
Several preset genomes are available. For organisms marked with an NCBI accession, the genome and annotation files will be downloaded automatically on first use. Other genomes (FASTA) and their annotations (GFF) can be downloaded from the NCBI website and uploaded using the "Own files" option, or by entering an NCBI assembly accession directly. For more details on how to download custom genomes, have a look at our help page.
Enter an NCBI assembly accession (e.g. GCF_000005845.2 for E. coli K-12). You can find accessions at NCBI Datasets. The genome FASTA and GFF annotation will be downloaded automatically.
GCF_000005845.2
Below, custom FASTA and GFF files of a bacterium of interest can be uploaded (can be downloaded from NCBI):
Upload a GenBank file (.gb, .gbk, .gbff) of the target organism:
Please add an ASO-sequence (ATGC-alphabet) below:
Control sequence type
Select the number of mismatches to introduce (must be even, as mismatches are generated by swapping pairs of non-equal bases).
Screen other genomes for off-targets (optional)
Select to screen for off-targets in the human transcriptome (FASTA) or the human microbiome (FASTA). For the human transcriptome, the whole transcriptome is screened, whereas for the human microbiome only translation initiation sites are considered. Note, that the selection of these additional screens will increase the running time of Scrambler
