Hello,

I'm looking for the diversity of homologous functional genes among 4 different environmental samples. To this end, I amplified them by PCR using degenerated primers (CODEHOP), cloned 96 amplicons per environmental sample in a plasmid, checked amplicon sizes by common amplification using specific plasmid primers, and finaly, sent 784 (4*96*2) large amplicons (targeted gene + part of the plasmid ; Forward and Reverse) to be sequenced by Sanger way.

My question (if you are still here) : how can I trim the common plasmid part from all my sequences, and build contigs, without doing it one by one ?

At least, thank you for your attention !