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This is probably a really stupid question but....
I'm trying to design an assay to be run on the Sequenom Mass Spectrometer instrument. I'm using their online design software tool and can't get past the first step- importing my reference seqeunces. I'm trying to create a somatic mutation assay, not a SNP assay, so I can't (I guess) just use RS numbers (which is easy because the software pulls the sequence from NCBI from the rs numbers). My other option is to paste or upload the sequence (with the mutation annotated in brackets ([WT/MU]). My problem is that I don't know how to retrieve these sequences... Am I supposed to individually search each gene/mutation in genbank, copy like 200bp of flanking sequence into a doc. file and manually bracket off the mutation and wild type nucleotides (I guess using the format that is retrieved from rs numbers as a guide)? Or is there a way to just pull that type of somatic mutation file from NCBI like with the rs numbers?
I'm not sure if I'm explaining this correctly... does any of that make sense?
Thanks in advance for any feedback.
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