I have tried in BLAST using forward and reverse primers as unique sequence separated by Ns but it does not recognize anything. Either, if I don't specify the organism in which the primer's sequence is, BLAST is not able to find the gene that should target, so I'm not confident on test specificity this way. I have also tried with BioEdit, but I don't know how to indicate that is a pair of primers to do alignments with several gene sequences. I would be really grateful if someone can help me with this.
Hi
you can try 2 ways, in the UCSC web server (http://genome.ucsc.edu/cgi-bin/hgPcr) or the NCBI one (https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome) to make in silico PCR.
I advice you to take some times in the UCSC since it offers many interesting tools for bioinformatics and genomics.
bonjour chez vous
fred
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