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.
For the preset genomes of Salmonella (substr. SL1344) (FASTA, GFF) and E. coli (K12) (FASTA, GFF) we provide a list of essential genes. For Clostridium difficile 630 (FASTA, GFF) and Fusobacterium nucleatum (ATCC 23726) (FASTA, GFF) we provide the newest genome files with annotations. 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
Select an essential gene in the dropdown menu
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
Number of maximally alowed mismatches for the off-target prediction algorithm. For 10-mer PNAs usually three or less mismatches should be chosen, as more mismatches prevent PNA binding. Up to 4 mismatches can be allowed
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 genome (FASTA) or the human microbiome (FASTA). For the human genome, 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
