Hypervariable regions in 16S libraries

Hi Pat,

For your (aligned) reference libraries, have you noted the locations of the Vj regions? Do you know where they start and they end?


I have them in a notebook somewhere but all my stuff is in boxes as I moved offices recently. If you want the coordinates for your sequence, take E. coli (or something) and trim it to your primer regions and then align it to sliva.bacteria.fasta and run summary.seqs. Viola there’s your start and end positions.


It’s as I feared. Well, I guess a little mindless work is rejuvenating, sometimes. Thanks.