Dear fellow UCSC users, since a while, while subcloning regions, I was fed up with designing primers manually with primer3. So I wrote a primitive little tool to design primers for regions of interest based on the UCSC browser infrastructure.
You simply copy-and-paste all regions of interest into a webform. The script will add x basepairs 5' and 3' and run primer3 with your parameters on it. You can select some of Invitrogen's Gateway-adaptors for the cloning (haven't added code for restriction enzymes yet). It will output your primers and their Tms pasteable into an excel file, the sequences to paste them into the BLAST-webforms to check the sequencing results later and another table which can be pasted into eurogentec's primer ordering form directly (this is our primer supplier). A demo is here: http://genome.ciona.cnrs-gif.fr/scripts/genomePrimers/genomePrimers.cgi The tiny 350-lines source code is here: http://genome.ciona.cnrs-gif.fr/scripts/genomePrimers/genomePrimers_b1.tar.gz It's based on emboss's eprimer3 which has to be installed on the machine. Perhaps this is useful for someone one day, it saved me quite a bit of time when testing regions for LacZ expression. A tool like this might represent a useful addition to the UCSC website one day (+restriction sites, +in-frame with selected gene model) and might be appreciated by those wet-lab biologists that commonly do not run high-throughput experiments. cheers Max _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
