direct sequencing vs sequencing of cloned PCR product

[kaps]

Dear all,

I would like to know which of the two is better, sequencing PCR product directly or sequence the PCR product after cloning?

[nucacidhunter]

It depends on downstream application. For consensus sequence PCR product sequencing would suffice because all possible variants or highly homologous regions will contribute to consensus. To identify SNPs or short indels cloning is preferred. Also for applications such as protein or transgene expression sequencing cloned fragments are necessary to make sure that sequences are error free and in correct frame.

[kaps]

Thanks nucacidhunter,

My interest is consensus sequence. I will then go ahead with PCR product sequencing.