Today I’m trying to get started on the new BLAST +2.81 that has new databases and improved performance. This is pretty exciting because once I figure out how this works, I’ll be able to easily get taxonomy information like Order, Class, etc. I’m attempting what I believe is the first step in this process: trying to get the taxid for “Decapoda”. Details below of resources used and what I did.

New BLAST nt taxonomy: Step 1- trying to get Decapoda taxid

BLAST +2.81 information

New BLAST taxonomy options

Sam installed the new version on Mox:
/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin
And the databases:
/gscratch/srlab/blastdbs/ncbi-nr-nt-v5

Sam reccommends that each user installs the eDirect utilities in order to use the full taxid functionality.
Instructions on installing eDirect: here

My eDirect directory (after installation) lives in my home directory on Mox:
img

Contents of eDirect:
img

The new BLAST taxonomy method starts with (this example was taken from the pdf):

get_species_taxids.sh -n Enterobacterales

Taxid: 91347
rank: order
division: enterobacteria
scientific name: Enterobacterales
common name:

1 matches found

get_species_taxids.sh -t 91347 > 91347.txids

blastn –db nt –query QUERY –taxidlist 91347.txids –outfmt 7 –out OUTPUT.tab

So, if I’m understanding this correctly, I am going to:

  1. run the first command:
    get_species_taxids.sh -n Decapoda

That will give me a taxid number, which I will:

  1. then use to create a file with the extension .txids that will contain the parts of the overall nucleotide taxonomy database that are included in that taxid number:
    get_species_taxids.sh -t ##### > #####.txids

  2. Then, I’ll perform a blastn with my query.fa (the assembled C. bairdi transcriptome) against the taxid list (file with extension .txids) to find all of the proteins that are associated with Decapoda, and put it into an output file (extension .tab).

Here’s what I have currently in queue on Mox:

#!/bin/bash
## Job Name
#SBATCH --job-name=get_species_taxid
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=4-00:00:00
## Memory per node
#SBATCH --mem=100
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=graceac9@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/graceac9/analyses/0115-get-species-taxids

# Load Python Mox module for Python module availability

module load intel-python3_2017

/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin \
-get_species_taxids.sh -n Decapoda
-out 0115-get_species_taxid_decapod.txt

Not sure if this will actually do anything… but we’ll see once Sam’s job finishes.

In the meantime…

Crab:

  • Extract RNA using Trizol LS Reagent tomorrow, run on Qubit, Bioanalyze with Qiagen kit-extracted sampels

2015 Oysterseed:

  • Work on figures and paper (Emma is coming to lab meeting Thursday - I will only be able to be there 9:45-10:15)