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PCR sequencing/cloning-seq for SNP identification - (Dec/30/2008 )

Hello all!! i am trying to find out if there is any polymorphism at a gene locus of cattle, the gene itself is 5 kb long. do you think the ideal strategy would be to sequence the pcr products directly or shud i go for cloning first? my plan was to go for cloning and compare it with a sequence available at Genbank (which is for a pure breed, whereas I'm looking at cross-bred cattle) and then go for RFLP. Someone please be kind enuf to comment.


Direct PCR product sequencing is good enough. If you clone and sequence, you have to sequence multiple clones.