Blast

Author

Chris Mantegna

Published

May 13, 2023

Blast Off!

The workflow to BLAST genetic sequences is similar regardless of type (i.e., genome, transcriptome, protein, gene, etc.). ‘Blasting’ a sequence is a fun way to compare your genetic data against the largest ‘crowd sourced’ database of reference genetic data available for free. Here we will walk through the process and a few things you can do to use with the data you find.

cd /home/shared/8TB_HDD_02/cnmntgna/Applications/bioinfo/
curl -O https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz
tar -xf ncbi-blast-2.13.0+-x64-linux.tar.gz

ls /home/shared/8TB_HDD_02/cnmntgna/Applications/bioinfo/

/home/shared/8TB_HDD_02/cnmntgna/Applications/bioinfo/ncbi-blast-2.13.0+/bin/blastx -h

cd ../data
curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
mv uniprot_sprot.fasta.gz uniprot_sprot_r2023_01.fasta.gz
gunzip -k uniprot_sprot_r2023_01.fasta.gz
ls ../data


/home/shared/8TB_HDD_02/cnmntgna/Applications/bioinfo/ncbi-blast-2.13.0+/bin/makeblastdb \
-in /home/shared/8TB_HDD_02/cnmntgna/data/uniprot_sprot_r2023_01.fasta \
-dbtype prot \
-out /home/shared/8TB_HDD_02/cnmntgna/output/blastdb/uniprot_sprot_r2023_01

curl https://eagle.fish.washington.edu/cnidarian/Ab_4denovo_CLC6_a.fa \
-k \
> /home/shared/8TB_HDD_02/cnmntgna/data/Ab_4denovo_CLC6_a.fa

head /home/shared/8TB_HDD_02/cnmntgna/data/Ab_4denovo_CLC6_a.fa
echo "How many sequences are there?"
grep -c ">" /home/shared/8TB_HDD_02/cnmntgna/data/Ab_4denovo_CLC6_a.fa

#fix my paths for reproducibility purposes, the full path is incorrect for that purpose
/home/shared/8TB_HDD_02/cnmntgna/Applications/bioinfo/ncbi-blast-2.13.0+/bin/blastx \
-query /home/shared/8TB_HDD_02/cnmntgna/data/Ab_4denovo_CLC6_a.fa \
-db /home/shared/8TB_HDD_02/cnmntgna/output/blastdb/uniprot_sprot_r2023_01 \
-out /home/shared/8TB_HDD_02/cnmntgna/output/Ab_4-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 20 \
-max_target_seqs 1 \
-outfmt 6

head -2 /home/shared/8TB_HDD_02/cnmntgna/output/Ab_4-uniprot_blastx.tab
wc -l /home/shared/8TB_HDD_02/cnmntgna/output/Ab_4-uniprot_blastx.tab

curl -O "Accept: text/plain; format=tsv" "https://rest.uniprot.org/uniprotkb/search?query=reviewed:true+AND+organism_id:9606"