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Old 04-09-2015, 11:49 AM   #2
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Location: CT

Join Date: Apr 2015
Posts: 243

the only way to compare across regions is to just taxonomically identify the sequences against the same database and compare the results. Depending on what your samples are and how well your organisms are represented in the databases, the results could be between mildly interesting and a waste of time. (I tried something like this on 454 sequenced deep ocean samples v8-9 vs v1-3, it was a waste of time). If you are trying to determine what region to use for a larger study, you're better off creating a database of full length sequences that are representative of your communities and doing the comparison in silico
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