# RESCRIPt for entire Blast Nucleotide database?

**URL:** https://forum.qiime2.org/t/rescript-for-entire-blast-nucleotide-database/27636
**Category:** Library Support
**Created:** [September 12, 2023, 1:37am UTC](https://forum.qiime2.org/t/rescript-for-entire-blast-nucleotide-database/27636 "2023-09-12T01:37:59Z")
**Posts on this page:** 1
**Showing post:** 5

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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [September 13, 2023, 2:30am UTC](https://forum.qiime2.org/t/rescript-for-entire-blast-nucleotide-database/27636/5 "2023-09-13T02:30:53Z")

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Hi @ahale004,

**RE 1:** RESCRIPt does not currently provide tools to directly download pre-formatted BLAST databases, e.g. ('nt'), which are located here [ftp://ftp.ncbi.nih.gov/blast/db/](ftp://ftp.ncbi.nih.gov/blast/db/). Using the full pre-formatted `nt` database would be much quicker than downloading and compiling yourself. You can, read up on [how to run BLAST locally](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata).

One of the other devs reminded me that we have been considering adding this feature to RESCRIPt via these relevant GitHub PRs:  
[https://github.com/qiime2/q2-feature-classifier/pull/191](https://github.com/qiime2/q2-feature-classifier/pull/191)  
[https://github.com/bokulich-lab/RESCRIPt/issues/135](https://github.com/bokulich-lab/RESCRIPt/issues/135)

But we do not yet have a time-line for when we'll be able to implement this. _Until then, I'd recommend a making several amplicon-specific reference databases. More on this below...._

**RE 2:** As far as I know, it is not possible to download the nucleotide BLAST database via a query.

**RE 3:** There are many ways to generate reference reads for use in `qiime feature-classifier classify-consensus-blast`, all you require is a way to construct a taxonomy.qza and a sequence.qza file. Some examples of which are [here](https://docs.qiime2.org/2023.7/tutorials/feature-classifier/).

* * *

**Making individual custom databases:**  
Have you read through the RESCRIPt tutorials as listed [here](https://github.com/bokulich-lab/RESCRIPt#using-rescript)? There are several ways by which you can use RESCRIPt to make specific custom amplicon databases using data from GenBank. For example, there is one tutorial for making a [trnL database](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618), and another tutorial that outlines a different approach, on constructing a [12S rRNA gene database](https://github.com/bokulich-lab/db-benchmarks-2020/blob/master/notebooks/Make-12S-rRNA-gene-db.ipynb).

-Cheers!

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