I need to design primers for qRT-PCR. The CDS sequences for the single target gene are given as chunks with differing base pair number. can i just combine the different CDS sequences of same gene into one single stretch of CDS sequence and design the primers accordingly ? If NO please explain the possible consequences of combining different CDS sequences.
Hi Pavani yes you can do like that, taking care of distinguishing the exons. or you go to the NCBI in silico PCR (https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome) or use the UCSC genome browser where you'll find an optional track with positions of published primers made for qPCR (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu).
fred
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