Hi
I want to design PCR primers for Infectious Bronchitis (IB) , Can any expert tell me
If the genome sequences that I will use it as input sequence for primer3 : CDS of the genome to be as cDNA ?
Regard to IB is positive single strand virus
If the virus is positive single strand ( i.e make as mRNA ) ,I will put the genomic as an input for primer3 then click on right primer and left primer: then it gives us the forward and reverse primers that used for amplification and one of them ( reverse primer ) used for cDNA synthesis to make double strand primer.
but my question is : if the virus single strand negative , do I need to make reverse complement sequence to keep our 5' and 3' ends properly oriented.
by EMBOSS revseq program so the result is sense template (- strand) so I can design primers as previous.
What gene or ORF you need amplified? for example for phylogeny you can use primers for region S1, if you want detect for qRT-PCR can use primers for the 5´UTR....
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