I am currently performing a sequencing experiment on a human gene of interest, where the gene is amplified using PCR. To verify performance of the PCR (number of artifacts etc), it would be good to amplify another locus with similar length and GC content. Can you recommend any tools for this purpose? For example, a possible query would be for a locus with a size of 10kbp and a GC content of 50-55%.
Does this control really help Manfredi Carta . It also matters what the distribution of the GC looks like. For instance all GC randomly dispersed would be expected to amplify but 1000 Gc consecutively would hairpin and loop and cause Taq much difficulty and probably need higher melting primers and the difference in primer annealing itself would have an effect on the number of mis incorporations in the amplimer. In answer to your question though unfortunately I do not know of a useful tool such as you describe.
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