Question: how to chose one 16s rRNA from each genome
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gravatar for akhilvbioinfo
2.0 years ago by
akhilvbioinfo100
India, chennai
akhilvbioinfo100 wrote:

 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
 

rna-seq gene • 613 views
ADD COMMENTlink modified 2.0 years ago by 5heikki6.6k • written 2.0 years ago by akhilvbioinfo100
1
gravatar for 5heikki
2.0 years ago by
5heikki6.6k
Finland
5heikki6.6k wrote:

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..

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by 5heikki6.6k
0
gravatar for Abdullah
2.0 years ago by
Abdullah90
Germany
Abdullah90 wrote:

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

ADD COMMENTlink written 2.0 years ago by Abdullah90
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