You dont really need a database to process the sequences. You can get OTU and later use Phymet2, to blast against mcrA database and get the taxonomy. And then manually do the graphics.

Abhijeet Singh

I used Qiime2 for 16S rRNA gene analysis, so it is needed to have the mcrA related database like SILVA database, which have two essential files called taxonomy and sequences, because I would like to have the same analysis processes that I have done for the 16S rRNA project in QIIME2 environment as well as the the graphs, plot!

Now, do you know how can I provide the mcrA database like SILVA?

Thanks

Making a database is a project in itself and it would take a lot of time. I made a database myself and its too time consuming. If you want to make yourself a new database, you are most welcome.

Abhijeet Singh

Thanks for caring! I did not think it take ages to generate a database.

At least, could you please tell me how can I do that? What is the protocol? Is there a standardized and clear approach?

In the near future, I will use dsrAB gene, so it would be helpful. I would like to know and to take advantage of your experience. Thanks for sharing in advance!

dear Xu Liu

Thanks! the sequences of mcrA gene were already downloaded from FunGene website. There is no any problm in catching sequences all in all. The issuse lays on taxonomic paths or taxonomy file. I do not know how to provide it or how to make by myself. Have you got any idea about it to provide it?

One of my friends and Otoniel Maya told me you should extract them via NCBI but I have no any protocol about it. By the way, I found mcrA databases in a paper which it is compatible with Mothur software pakage. I used it in Qiime2 I was unsuccessful cus classifier gave errors except Blast plus. The taxonomy barplot I achived from Blast plus was not relaible because they were just 12 taxonomic paths focused on phylum, not down levels!

Thanks

Xu Liu

Otoniel Maya

In FunGene website there are two options before downloading the sequences: 1. aligned 2. unaligned

Which one should be downloaded? I previously downloaded the unaligned. i want to know Did I download the right one? If yes, what is the use of another version (aligned sequences). Could it be problematic if I use aligned sequences?

Another question in this case is should I modify the sequences becaus it has descriptions? Or no need?

Thanks

Mehrdad

Hi if you want to make your database just use this script! It will be fast and easy!

https://github.com/bakerccm/entrez_qiime/releases