Hi,
Could you please clarify this query:
if 426bp amplified for mtDNA D-loop (control region) and after editing/trimming primers finally get about 419 or 400bp. So is it correct if proceed final analysis with 419bp or 400bp sequences?
Thanks,
Dear Ahasan,
If your primers are specific, then no need to worry. Go for sequencing for single product just to confirm your interested sequence. So that you can go for the large sample size.
All the best.
Hi Ahasan, It is common practice to trimm the primers from the amplicon sequence before starting with sequence analyses like BLAST and phylogenetic comparisons. Primers are usually able to bind also to slightly dissimilar sequences (eg. a few bp mismatches) and you wouldn't recognize these differences because they are hidden by the sequence of the primers. Therefore, primer sequences are trimmed and you work only with the "native" sequence of the fragment. Sometimes I leave the primer sequences until sequence alignment (eg. in MEGA) and then trimm the primer sequences from the whole alignment. Hope I could help you. Cheers, René
thanks all. So, after trim off primer sequences, if base paris is less than 426bp (in my case, it was amplified) it's no problem? but it should be 426bp, isn't it?
thanks,
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