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Small undergraduate research project - (Oct/02/2005 )

Hi everyone,

I'm a 3rd year biology student and I'm researching for my bioinformatics research project. The subject of my project is primer and probe design. It's going to be a poster that will illustrate the concepts behind designing effective general primers and probes.

One of the requirements of this project is that I use 3 "offcial" resources, meaning either research publications or books. I'm having a little trouble finding them as our school library does not hold anything of that specific subject, and my efforts using search engines have proven fruitless.

If some of you experienced folks could point me in the right direction in finding some solid publications that will describe primer/probe design concepts, it would help me a lot.



Is there a particular language you're going to work in, or are you just looking for theory and principles?


u will not find anything reliable using google or other general seach engines. Check out and combine it with the impact factor lisitng available at

I consider anything above a 3.5 as a solid journal. ....This is only for journals though


I'm looking for pretty much all the theories and principles that are involved in good primer/probe design.

How do I combine pubmed with the impact factor listing? I tried pubmed, but all I got were very very specific studies. I think this kind of knowledge is assumed when conducting research; it's like searching for "how to sequence DNA."


toots, you might be more able to find something helpful if you go the website of a vendor and find a tutorial offered by that vendor. For example, Qiagen, Promega, Applied Biosystems, and others are all likely to have some sort of downloadable tutorial on primer design.

here's the kicker: look at the references in the tutorials. this will tell you which papers will be useful to you. you don't really need to know about specific drosophila primers involved in the cloning of toll receptors or something crazy like that...but hopefully you can find some good general rules, and get references to lead you to the specifics

use the journal ranking list that pria gave you to determine which references are really "expert"

good luck


Try Current Protocols in Molecular Biology.

I am not sure whether your school library hold it.

Or other laboratory maunal on Molecular Biology.

-Minnie Mouse-

On a related note, has anyone run across a primer program that will automatically sort out primer-dimer and hairpin results? Every program I've run across will generate primer pairs, but then you have to plug it into another program or module in order to analyze those pairs.

I was actually in the process of writing such a program in Perl, but I haven't had much time to work on it.



i would buy that software!

wow, get a patent quick, you could make millions and live out the rest of your life on the beach somewhere...