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Old 09-10-2015, 11:50 AM   #3
danova
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Location: France

Join Date: Sep 2010
Posts: 27
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Hi Brian,
At the end I want to see if my degenrated primers (or the sum of the oligos as you suggest) match the same 16s. That will tell me the coverage of my primers in my 16s database.

Indeed that looks like a valid option. As you suggest i can align both separately and then combine primers that match the same 16s , check the distance between the primers to satisfy the 800 to 1500 nt in between. Then i guess extract the aligned sequences (start -end positions of the alignement).

IŽll give it a try,
thanks,
david

Last edited by danova; 09-10-2015 at 11:54 AM.
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