EMP, GreenGenes - Make Local DB and BLAST

Create a reference database from my GreenGenes + 16S strains

I used the rep_seqs that were generated when I created my phyla tree as my database.
Made a new file - curto-db.fasta
*these are aligned rep_set seqs

Two ways to create your own local database:

1.   Use the BLAST command line

The sequences need to be in a specific format:

Ex.
>gnl|831711|Microbacteriaceae_Candidatus_Rhodoluna
DNA here

makeblastdb
$ makeblastdb -in curto-db.fasta -dbtype nucl -out curto.db

Find out more details HERE

2. Use Geneious

Tools -> Sequence Search

Window pops up and click "Add/Remove Databases" - select "Add Sequence Database"
Follow instructions (ie. select 'nucleotide' and 'custom BLAST')

Perform Sequence Search again, but this time Select "Database" and scroll to your new custom database!

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Next, BLAST the EMP seqs against my local database.
*The EMP seqs were generated from QIIME assign_taxonomy.py and took those who identified with Curtobacterium with greater 0.67 quality score
*The seqs are also extremely short - less than 200 bp

Export the data to a .txt file

Really strange results - EMP seqs hit rep_seqs at equal frequency

Need to look at seqs in Geneious and check alignments!