For faster mapping of many sequences against the same reference database Example: create E. coli genome DB# merge all E. coli reference genomes into one ecoli.fasta file
# create blast databasecat genomes/ecoli_strains/*.fna > ecoli.fasta makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl -parse_seqids is required to identify gene/contig IDs in mapping hits -dbtype specifies the type of sequences: protein 'prot' or nucleotide 'nucl' # Blast using species DB (option: -db) blastn -query genes.fasta -db ecoli.fasta -outfmt 6 -evalue 1e-30 http://www.ncbi.nlm.nih.gov/books/NBK279688/ |
Generate_database
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Public sequences