For Biology Grad Students-What can we learn from BLAST about primers?

I'm not a biology graduate student, but I know that BLAST takes a given sequence and finds similar sequences in a database.  I might be able to help you, but I only know how BLAST works, not how it's used in biology.  I'm wondering -- do you know how/why a primer will hybridize against a sequence?  If you know that and tell me, I might be able to help you with BLAST question better.

fellow bio-comrade,
yes, u get the homology hits. But what that means is that if your primer is  homolgous to some other part in one strand of the dsDNA, it can then hybridize with the other strand in the dsDNA. Thus, u don't want it to be homologous to any other part of either strand.

I think you are looking at the results correctly, but I think if your getting tons of hits, you need to re-design your primers (I'm assuming your doing PCR).  You will need at least one primer to be totally unique.

Sometimes I will use BLAST for the same purposes as you (PCR), and will get many "hits" using BLAST.  But the amplicon sizes of the other hits are very different in size than the expected amplicon size I hope to amplify.  Sometimes this is OK.

For instance, the amplicon I want is 1000bp.  The majority of other amplicons that will amplify in the PCR are around 200bp (I know this from BLAST).  I could separate out the junk amplicons and isolate the amplicon of my interest by "Low Melting Agarose" gel electrophoresis, cut out the band of interest, and isolate and purify it.  

In short, getting tons of "hits" on blast can sometimes be overcome by employing additional isolation methods.

Here are some other tips:

When performing a blast, make sure you choose the genome of your choice (i.e. human).  

The colored bars give you an idea of the size of other potential amplicons.  Click on the bar to take you to the sequence analysis.

The sequence data (below the colored bars) shows the homology of the primers.  The most critical part of the primer is the 3' end of each primer.   Re-design your primers if the 3' ends shows too much homology in BLAST analysis (by extending your primers by a few base pairs).  Then BLAST again.

Use high annealing temperatures in the PCR to help eliminate un-wanted amplicons.

Again, this is just good for PCR.  

Hope it helps.  Pass on the good Karma!