Hello Max, Thank you for sharing the tools you have developed with the UCSC Genome Browser community! Please feel free to add this to our genomewiki at http://genomewiki.ucsc.edu, in the User Developed Scripts category: http://genomewiki.ucsc.edu/index.php/Category:User_Developed_Scripts
-- Brooke Rhead UCSC Genome Bioinformatics Group On 10/31/08 07:42, Maximilian Haeussler wrote: > 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 _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
