Is it wrong to use 16s rRNA sequences of strains other than the one you want to include in your phylogenetic tree?

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Mahadev Asaram Jadhav

Dear pejvak,

You can retrieve 16S rRNA sequences of Bacteria, Archaea and Eukarya by accessing Silva database.plz visit

http://www.arb-silva.de/

u can download 16S rRNA sequences of all strains of bacteria or whatever may be very easily. then u can create phylogenetic tree.

Pejvak Moghimi

Dear Mahadev,

I downloaded the latest file, which is 290 MB compressed and 3.5 GB once oppened. This took a very long time to open in a multiple allignment tool and to no end, as the sequence titles were just a bunch of codes, for which I found no database with corresponding names. Any suggestions?

you can copy the above mentioned website and paste into URL.

.then u can search sequences according to species name,accession number, strain,publication ID. it also provide facility to submit sequences for alignment.

try it.

I have tried it before and tried to find the sequenses I am looking for in the "browe" section of the website but it didn't have the strains I was looking for neither. Frankly either I am looking in the wrong section or this website is nowhere nearly as complete as it claims to be, as I couldn't find some common strains. I could give you some examples if that helps to clarify whether it's my mistake.

Dear Pejvak,

you can try "Search" option instead of Browse. plz specify the name of species and its strain. plz provide it for future communication.

I finally figured out how to do it, though I have to say the database is a bit strange. Thank you so much for your time.

Marina Yurieva

There is not really strain information in Silva database, it's even hard to rely on their species either. But this is the way with most of the available databases. If you want to go down to the strains you most likely have to build your own. Plus, if you use QIIME for your analysis you need to adjust an OTU threshold because default is 97% and that won't even give you all the species, not mention any strains.