how to chose one 16s rRNA from each genome

Question

[Eva_Maria]

I predicted all 16s rRNAs using rnammer. For each genome there is more than two 16s rRNAs.. So how to choose one 16s RNA for each genome form this? In what base? The selected 16s RNAs will used to MSA and phylogeny analysis

Answer 1

[5heikki]

You could cluster them and apply the same criteria for choosing the representative sequence in all cases, e.g. most abundant or centroid. Or you could just pick the longest, random, the one with the highest score against the hmm, etc..

Answer 2

[Abdullah]

one suggestion would be to take them all and make a consensus sequence out of them, and then use this for further analysis.