I am not working at UCSC but you can also paste your regions into my genomePrimers script (it will then get the sequences, run primer3 from http://frodo.wi.mit.edu/primer3/ on them) and output the primers:
http://genome.ciona.cnrs-gif.fr/scripts/genomePrimers/genomePrimers.cgi cheers Max On Fri, Jan 15, 2010 at 11:00 PM, Jennifer Jackson <[email protected]> wrote: > Hello, > > Have you seen the PCR tool in the Browser? > > follow the links to: > http://genome.ucsc.edu/ -> left blue nav bar "In Silico PCR" > > or directly, > http://genome.ucsc.edu/cgi-bin/hgPcr > > Choosing regions will still be your decision, but this tool can help with > analyzing the selections under consideration. > > Here is a link I found that is quite informative with plenty of general PCR > design advice, all in one place (ignore the article header, the leading > "novice" parts are quickly replaced with hard biology): > http://www.squidoo.com/primer-design > > Other similar results (wiki, etc.) come from a google with the search term > "PCR Primer Design", but the one above seems like a good place to start for a > re-fresher or to catch up with the latest methods. > > We hope this helps, > Jennifer > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Indrani Datta" <[email protected]> wrote: > >> From: "Indrani Datta" <[email protected]> >> To: [email protected] >> Sent: Friday, January 15, 2010 8:32:39 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] Desinging primers for CpG islands >> >> Hello, >> >> Assembly “hg18”, March 2006 >> RefSeq Genes >> >> I am trying to design primers for some specific genes for >> methylation. >> I know in Table browser for March 2006 , human assembly , >> under regulation, I can download the sequences for CpG islands for >> specific regions ( specific gene regions). >> >> But I need some more information how can I related this >> sequences for primer design. >> >> I would really appreciate any information. >> >> >> Thanks in advance, >> Indrani >> ============================================================================== >> CONFIDENTIALITY NOTICE: This email contains information from the >> sender that >> may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise >> protected >> from disclosure. This email is intended for use only by the person or >> entity >> to whom it is addressed. If you are not the intended recipient, any >> use, >> disclosure, copying, distribution, printing, or any action taken in >> reliance >> on the contents of this email, is strictly prohibited. If you received >> this >> email in error, please contact the sending party by reply email, >> delete the >> email from your computer system and shred any paper copies. >> >> Note to Patients: There are a number of risks you should consider >> before using >> e-mail to communicate with us. See our Privacy Policy and Henry Ford >> My Health >> at www.henryford.com for more detailed information. If you do not >> believe that >> our policy gives you the privacy and security protection you need, do >> not send >> e-mail or Internet communications to us. >> ============================================================================== >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
