I use DNAstar from Lasergene and it works quite well. Primer3+ is also a very good alternative; but I think the best ones are those handmade !!!
I think primer 3 plus is the best tool. I have designed primers using primer blast as well. Both tools are good.
Primer 3 Express and OLIGO 6 are tools that I found useful. Hope it does for you too.
However, it must be kept in mind that at best they support the primer designing process and no substitute to common sense and experiences of a researcher, given the complexity and not-so-reliable nature of PCR experiments in general.
I use to select primers with Primer3.0 and then, I check the presence of hairpins, hetero- or self-dimerization with the OligoAnalizer software, http://eu.idtdna.com/analyzer/applications/oligoanalyzer/default.aspx?gclid=CKGa6Nyl7bgCFfMbtAodvFoAYg
I've used Primer 3 several years ago. Also, I've used the Oligo analyzer tool available on the IDT website (Integrative DNA Technology) during my post-doctoral years in the US. My research scholars are now using a software called Primer X. Good luck.
Primer3Plus.. http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/
Http://xtal.nki.nl/ccd/start_ccd.html
this will run a few prediction methods, so that u can select from all protein residues you want to use in that construct.
It is a one click method
I am used to use Primer3. Then I check the primers in UCSC using the option PCR. Here you paste the primers and then UCSC check whether or not the primers recognize the DNA region that you are interested in (Sepecies specific search). Usually it works well. I have never get any problems.
Good luck
I recommend four tools for primers design
Primer Design Tool http://www.operon.com/tools/oligo-design-tools.aspx
Primer3Plus http://primer3plus.com/cgi-bin/dev/primer3plus.cgi
PrimerX http://www.bioinformatics.org/primerx/
Primer-BLAST http://www.ncbi.nlm.nih.gov/tools/primer-blast/
Although all are good tools, the best tool for me is Primer3plus.
http://bioinfo.ut.ee/primer3-0.4.0/primer3/.. usually our lab used these site..but u do have to careful about some properties while designing.. i upload my file here
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools