# Suggestions for using nifH ARB database for taxonomy assignment in QIIME2

**URL:** https://forum.qiime2.org/t/suggestions-for-using-nifh-arb-database-for-taxonomy-assignment-in-qiime2/14694
**Category:** General Discussion
**Tags:** taxonomy
**Created:** [April 29, 2020, 1:52pm UTC](https://forum.qiime2.org/t/suggestions-for-using-nifh-arb-database-for-taxonomy-assignment-in-qiime2/14694 "2020-04-29T13:52:38Z")
**Posts on this page:** 1
**Showing post:** 2

<div class="post-metadata">

### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [April 29, 2020, 2:54pm UTC](https://forum.qiime2.org/t/suggestions-for-using-nifh-arb-database-for-taxonomy-assignment-in-qiime2/14694/2 "2020-04-29T14:54:34Z")

</div>

Hi @vkk_24!

> [@vkk\_24](#):
>
> Currently there is no QIIME compatible sequence and taxonomy reference database available for nifH functional gene.

Not one that we release on the QIIME 2 website, but others must be out there, since there have been a few forum users who report using nifH in QIIME 2.

> [@vkk\_24](#):
>
> There’s a nifH gene sequence database constructed by [_jzehr lab_](https://wwwzehr.pmc.ucsc.edu/nifH_Database_Public/) which is in .arb format. My question is how to use such kind of databases which are in arb format to assign taxonomy. Is there any specific tool or method?

I recommend contacting the makers of that database to ask them if they have any ideas, they would have the best advice on how to convert to fasta and extract taxonomy information. They might even be interested in making a Q2 compatible release...

> [@vkk\_24](#):
>
> Can anyone suggest me or guide me as to how can I do taxonomic assignment for nifH amplicon data ?  
> OR  
> How can I construct a QIIME compatible reference sequence and taxonomy database for nifH gene?

Here is another forum topic that is pretty similar to yours and answers at least the second of these questions (and requires starting with fasta). It sounds like @EGvibrio was using a custom database — nevertheless, perhaps @EGvibrio has some advice or has worked with the jzehr nifH database? :

> [@How do i create a taxonomic table from fasta file?](https://forum.qiime2.org/t/how-do-i-create-a-taxonomic-table-from-fasta-file/13900):
>
> Hello everybody, I am a new QIIME2 user. I want to work with functional genes and I am starting with the nifH gene (dinitrogenase reductase) Recently, I downloaded the database (fasta file) but the database didn't come with the taxonomic table and the database comprise only a code name and sequence: Name sequence Therefore i can't use QIIME without a taxonomic table and I want to create a new one. I tried to find commands how to create a table on QIIME2 or search on this forum but I didn't…

I have not worked with nifH personally, but know of some nifH mock communities on [mockrobiota](https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-27), where the contributor recommended another nifH database released by jzehr, so maybe this would be something useful?: [https://wwwzehr.pmc.ucsc.edu/CART\_model\_public/](https://wwwzehr.pmc.ucsc.edu/CART_model_public/)

Let's see if @EGvibrio or others who have worked with nifH might have any advice!

---

_[View the full topic](https://forum.qiime2.org/t/suggestions-for-using-nifh-arb-database-for-taxonomy-assignment-in-qiime2/14694)._