ASO-checker is an accompanying tool to MASON which can be used to generate scrambled sequences for ASO-sequences. The algorithm takes in ASO sequences of lengths 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 sequences.
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.
Select the preset genomes of Salmonella (substr. SL1344) (FASTA, GFF), E. coli (K12) (FASTA, GFF), Clostridium difficile 630 (FASTA, GFF) and Fusobacterium nucleatum (ATCC 23726) (FASTA, GFF). Other genomes (FASTA) and their annotations (GFF) can be downloaded from the NCBI website and uploaded using the "Own files" option. 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):
Please add an ASO-sequence (ATGC-alphabet) of the ASO that you want to scramble below:
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
