I have both forward, reverse and probe sequences and I want to calculate accurate base pair length to check band for PCR products.
(Forward primer)nnnn(Reverseprimmer) is not work in blast.
I know my target gene nucleotide and the length of this sequences does it mean base pair that I want to check for band in PCR product?
For example my target sequences is AGTCAGCT and bp is 8
Is the right ideology?????
You cannot use NNNNs between primers to search because that will only find sequences of that size. Blast the primers as a pair at primer-blast
https://www.ncbi.nlm.nih.gov/tools/primer-blast/ making sure that you have selected the correct genome/species
I agree with Dr Rutland, you can also apply Insilico Pcr to predict the base pair.
You can also choose the genome to use for BLAST. No need to include all DNA sequences from everything if you are using just an organism with a sequenced genome (e.g. mouse, human, maize, etc.)
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