primer design - checking off-target site - (Jun/04/2005 )
How can I check whether my primers anneal to another site in the genome rather than my target site? (e.g. Human Genome)
Dear miyametu,
One good way to check your primer specificity is to BLAST your primer sequence against NCBI database.
How to do that?
First go to NCBI "http://www.ncbi.nlm.nih.gov/" --> select BLAST -->
nucleotide-nucleotide BLAST --> insert your primer sequence into the blank form --> click BLAST --> click format --> finally read result : ) simple
Good luck
Hadrian
One good way to check your primer specificity is to BLAST your primer sequence against NCBI database.
How to do that?
First go to NCBI "http://www.ncbi.nlm.nih.gov/" --> select BLAST -->
nucleotide-nucleotide BLAST --> insert your primer sequence into the blank form --> click BLAST --> click format --> finally read result : ) simple
Good luck
Hadrian
Hey,
When blasting should we also paste the human genome sequence too or just our primer sequence?
The UCSC genome database provides a very useful in silico PCR tool http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg17
Another similar tool called virtual PCR can be found here http://grup.cribi.unipd.it/cgi-bin/mateo/vpcr2.cgi
Anyone who can answer my question?
Thanks!
If you have actually visited the link given, you will know.