I want to identify a bacterium so i extracted DNA, amplipied and sequenced but now when i am doing blast the similarity is 97% I want to know what is the minimum similarities for comparing and making pylogenetic tree??
Less than 97% of similarity will imply you have different OTUs and therefore, putatively different species.
When blasting, I would recommend to have a look on best E-values more than similarity. However, the best E-values will come with the highest similarity percentages.
If you are looking forward to make some phylogeny I would recommend to download the 5 most similar sequences to each of your query and then run the phylogenetic analyses with different methods (ML, Bayesian...) and compare the results
just to mention, make sure that you have full length of the 16s rRNA sequence, and to compare the sequence with type materials when you do BLAST analysis. 97 seems to be relatively low percentage but this still depends on the species
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA