ASO-Checker is an accompanying tool to MASON which can be used to check different attributes of a pre-selected ASO. The tool takes ASO sequences and checks for several important sequence- and target-species related attributes. Similar to the MASON algorithm, it screens for off-targets and evaluates whether the sequence is suitable for further use.
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 one of the preset genomes or use "Own files" to upload your own genome. Some presets include essential genes that can be selected as target genes. For organisms marked with an NCBI accession, the genome is automatically downloaded on first use. 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 ASO-sequences (ATGC-alphabet) of the ASOs that you want to be checked below. You can paste plain sequences (one per line) or use FASTA format (max. 10 sequences allowed, length 8-14 bases):
Provide a locus tag to validate that your ASOs target the gene's translation initiation region (TIR). This enables MASON-style output with heatmap, secondary structure plots, and melting temperature barplot.
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 ASO-Checker
