Primer-BLAST combines primer design (using Primer3) and a specificity check with BLAST.
Primer-BLAST was developed to help users make primers specific to a PCR template. Primer-BLAST combines primer design (using Primer3) and a specificity check via a BLAST search. The specificity check against user selected databases can avoid primer pairs that amplify targets other than the input template. Primer-BLAST can also used with pre-designed primers. To get started with Primer-BLAST go to http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastN... and enter FASTA, an accession or a GI into the PCR Template box. Or alternately fill in the forward and reverse primers in the "Primer Parameters" area. By default human sequences are searched in the specificity check, but that may be changed to other organisms in the " Primer Pair Specificity Checking Parameters". Use the "Get Primers" button at the bottom of the page to submit your search. Please send question and comments about Primer-BLAST to blast-help@ncbi.nlm.nih.gov
