Hi,
I am doing molecular identification of my samples (cyanobacteria) using ITS and 16s gene sequences. For ITS region, once i BLAST my sequences against the NCBI data it just showed 94% similarity with other cyanobacteria. Is 94% similarity is acceptable?I am also building phylogentic tree using Mega6 and Mr. Bayes. I would like to ask should i use ITS sequences or 16s sequences to build a phylogenetic tree?
Thank you
I guess your question has been answered very well before, you can see this thread here,
https://www.researchgate.net/post/What_is_the_acceptable_percentage_similarity_of_BLAST_nucleotide_sequence_that_could_suggest_a_novel_organism
Hi Zoya,
94% simillarity is a very abstract measure, you have to team it up with the total query coverage and E value of the hit. If all these three parameters are satisfactory then you may comment on homology for a particular sequence.
Further I believe, that ITS sequences have not been an accepted marker beyond the genus level (Please Check) and thus a proper phylogenetic analyses is best performed using 16s rRNA sequences.
Hope this helps.
Best Sayak
ITS is too variable to be phylogenetically informative. Even in mycology, where ITS is used daily, it is only used as barcoding marker and for making trees within a genus.
Standard in bacteria is 16S rRNA gene. Other genes may be used when dealing with species from species complexes.
By the way I think IGS is much more used than ITS in bacteria.
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