Generate BLAST database

Create a blastn custom database

For faster mapping of many sequences against the same reference database

Example: create E. coli genome DB (species specific)

# merge all E. coli reference genomes into one ecoli.fasta file

cat genomes/ecoli_strains/*.fna > ecoli.fasta

# create species genome database for Blast

makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl

        -parse_seqids   is required when FASTA header IDs follow the bar-delimited NCBI format  >gi|129295

        -dbtype nucl    specifies the type of sequences: protein 'prot' or nucleotide 'nucl'

# run Blast using the created species DB  (database option:  -db)

blastn -query genes.fasta -db ecoli -outfmt 6 -evalue 1e-30

→  BLASTn output format 6

→  E-Value & Bit-score

https://www.ncbi.nlm.nih.gov/books/NBK569841/

https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.makeblastdb_application_opt/

> Public sequences