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Frameshift mutation in DNA sequencing? - (Oct/02/2013 )

I've got trouble in analyzing DNA sequencing. 


I sequenced PCR products with forward primer or reverse primer, and now I analyze these results. I compare them with NCBI genbank genome  to study polymorphic gene, and find some mutations.


I want to ask you: "Can I find the frameshift mutation if I compare them with NCBI genome?", because you know that there are some disruption at the beginning and the end of  PCR products sequencing . I think myself it's very difficult


Thank you very much


Hi Junvn, 


Yes, you should be able to spot a frameshift mutation as well. Although your read will have disruptions in the beginning and the towards the end, an insertion or deletion of a nucleotide will be picked up, when you compare your read to the reference sequence. 


There are some software that do this job for this or even a BLAST search of your FASTA sequence should show you the difference, if there is any.


However, it is best that the nucleotide where you are expecting this frameshift to be, is located somewhere in the middle of your read and not near the ends of the PCR product. 



-Ameya P-