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 most preset organisms we provide a list of essential genes that can be selected as target genes. 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):
For example: SL1344_1133, SL1344_P3_0012 for Salmonella SL1344. Locus tags of genes can be found in the GFF file in the 9th column, following "locus_tag=", see help page. Please select no more than 5 genes at once to keep the running time low
Length of bacterial ASOs is usually chosen to be between 9-12 nucleobases to enable entry into the cell. Length needs to between 7 and 16 bases
If not specified, all ASOs overlapping the start codon are designed. If a SD sequence exists, it can be useful to design more ASOs lying upstream (5') the CDS to inhibit translation
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 MASON
The random forest model was trained on 9-mer ASO data targeting genes in uropathogenic E. coli (UPEC). The predicted MIC values should not be interpreted as absolute values. Instead, use the MIC ranking to compare and select ASOs relative to each other.
