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
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:
