How to build 16S rRNA matrix?

Question

[buce_buper]

Hi all,

I have one question, "how to build 16S rRNA similarity matrix?".

I am trying to reclassify a family of bacteria, but inorder to do that I need to blastn multiple 16S rRNA sequences againts each other to build matrix, about 400 sequences. I use blastn, but the result did not give me any matrix. Is there any other method to do this? or I am missing something here.

Thank you for taking time to reply,

Best Regards

Buce,

[Asaf]

It's not really cleat what you are trying to achieve. What is your starting point? Generally there exists a multiple sequence alignment of all bacterial 16S in databases like Silva or GreenGenes