Working on functional gene- providing a database


(Meha) #1

Dear Friends,
According to my knowledge, Qiime1/2 is used for analyzing 16S rRNA and 18S rRNA.These genes are housekeeping, as you aware. Now, if a researcher decides to work on functional gene, such as mcrA, how can he provide a database? Do you have any suggestion?
Thanks a lot


(Nicholas Bokulich) #2

QIIME 2 is not specific to rRNA genes… many users commonly use other coding and non-coding marker genes, e.g., COI, ITS, even some functional genes like nifH, etc.

You need to find or construct this database, e.g., by compiling known reference genes. That database will need to be formatted the same way as other databases that are commonly used by QIIME 2 — so take a look at the greengenes or SILVA reference database to get an idea of what these formats are (fasta sequences and tab-delimited, semicolon-separated taxonomies in a text file).

Good luck!