BLAST biomin genes
Potential biomineralization targets of miRNAs
Investigating if any biomineralization genes are targeted by miRNAs in four species (AST, ACR, POC, and POR). A biomineralization protein list was created by FS (primarily from Stylophora pistillata). To see if any of the biomin genes are targeted by miRNAs, I am going to blast the biomin protein list against the protein fasta files for each species.
cd /data/putnamlab/jillashey
mkdir biomin_blast
cd biomin_blast
The sequences in fasta format are already on the server here: /data/putnamlab/jillashey/Pacuta_HI_2022/data/blast.
nano biomin_blast.sh
#!/bin/bash
#SBATCH --job-name="biomin_blast"
#SBATCH --nodes=1 --ntasks-per-node=20
#SBATCH -t 100:00:00
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --mem=100GB
#SBATCH --error="blast_out_error"
#SBATCH --output="blast_out"
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/Pacuta_HI_2022/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
module load BLAST+/2.9.0-iimpi-2019b
echo "Make blast dbs for ACR, AST, POC, POR" $(date)
makeblastdb -in /data/putnamlab/jillashey/Astrangia_Genome/apoculata_proteins_v2.0.fasta -out /data/putnamlab/jillashey/biomin_blast/AST_prot -dbtype prot
makeblastdb -in /data/putnamlab/jillashey/genome/Pmea/Pocillopora_meandrina_HIv1.genes.pep.faa -out /data/putnamlab/jillashey/biomin_blast/POC_prot -dbtype prot
makeblastdb -in /data/putnamlab/jillashey/genome/Peve/Porites_evermanni_v1.annot.pep.fa -out /data/putnamlab/jillashey/biomin_blast/POR_prot -dbtype prot
## not sure where ACR protein fasta file is
echo "Blast biomin seqs against protein dbs" $(date)
blastp -query /data/putnamlab/jillashey/Pacuta_HI_2022/data/blast/Biomineraliztion_Toolkit_FScucchia_ZDrefmt.fasta -db /data/putnamlab/jillashey/biomin_blast/AST_prot -out /data/putnamlab/jillashey/biomin_blast/AST_biomin_blast_results_tab.txt -outfmt 6 -max_target_seqs 2
blastp -query /data/putnamlab/jillashey/Pacuta_HI_2022/data/blast/Biomineraliztion_Toolkit_FScucchia_ZDrefmt.fasta -db /data/putnamlab/jillashey/biomin_blast/POC_prot -out /data/putnamlab/jillashey/biomin_blast/POC_biomin_blast_results_tab.txt -outfmt 6 -max_target_seqs 2
blastp -query /data/putnamlab/jillashey/Pacuta_HI_2022/data/blast/Biomineraliztion_Toolkit_FScucchia_ZDrefmt.fasta -db /data/putnamlab/jillashey/biomin_blast/POR_prot -out /data/putnamlab/jillashey/biomin_blast/POR_biomin_blast_results_tab.txt -outfmt 6 -max_target_seqs 2
echo "Blast complete!" $(date)
Submitted batch job 361991
Following the BLAST, the results in the .txt file will need to be compared to the miranda results for each species to see if the genes are targeted by any miRNAs.
The miranda data is comparing the 3’UTR sequence to the mature miRNA sequence, invoking strict binding.