Entering edit mode
4.8 years ago
Ömer An ▴ 260
I would like to find 12-mer short DNA sequences which do not map to the human genome and do not form self-mer as well. I want them to be as unique as possible. How can I get them? Which tool/software should I use?
"Self-mer" in this context would mean homodimerisation.
The only 2 ways to really assess this would be to use primer design software (since I suspect this is a primer design question anyway) and do some thermal calculations. A brute force way would be to simply check for 'palindromicity'.
Simple way would be to use https://eu.idtdna.com/calc/analyzer/home/batch but you're limited to 200 sequences at a time. Maybe check out Primer3 for a commandline tool.
Both comments are very useful. I generated all possible 12-mers in R:
I was thinking to "map" them to the reference genome with BLAT and pick the unmapped ones, but fragmenting the genome also sounds a good idea.
Edit: I finished the analysis: I used
jellyfishto fragment the human genome (hg19) for all 12-mers present, then used bash
commto get the difference between the two:
Now let the biologist dig into 168199 candidates to pick the best primers 😄