Question about BLAST database

Question

[ali.shojaee.bakhtiari]

I need to run blast against mouse genome to cancel mouse related strings in a set of 16S Amplicon reads.

Could someone please tell me which of the files in the following link should I put as the database for blastn

basically blastn -db ** ........

* I understand should be one of the following files or its unzipped format :

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001635.7_GRCm38.p5

[Farbod]

Dear Ali, Hi

The genomic.fna.gz file is FASTA format of the genomic sequences in the assembly.

Also have a look at Mouse in Genome Browser or ENSEMBL and Online Resources For Mouse Research and the answer in this post, please.

~ Best

[ali.shojaee.bakhtiari]

Thanks Farbod Quick question. Do you know if blastn can read through gz files or do I need to unzip them first?

[Farbod]

Ali Jan,

As you must use -makeblastdb to convert your database (here mouse genome) to a blastable database, I guess you must decompress your .gz file first.

of course it seems that it could be done in just one script as :

gunzip -c mouse-genome.gz | makeblastdb -in nucl

Have a look here please.

~ Best

[ali.shojaee.bakhtiari]

Thanks Farbod. Guess you came to my rescue :) The BLAST documentation seems to be extensive but quite misleading.

Answer 1

[GenoMax]

You should use bbsplit from BBMap to separate the mouse reads away from your metagenomic data. It would be immensely more efficient. Directions for use are here: BBSplit syntax for generating builds for the reference genome and how to call different builds.