BLAST is a software tool for searching similarity in nucleotide sequences (DNA) and/or amino acid (protein) sequences.
https://blast.ncbi.nlm.nih.gov/
https://blast.ncbi.nlm.nih.gov/BlastSearch → help.pdf → guide
https://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html
http://www.genome.jp/tools/blast/
https://blast.ncbi.nlm.nih.gov/blast/FAQ
Blast results
blastn -query genes.fasta -subject genome.fasta -outfmt 6
Blast database
makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl
→ Bowtie2 to map short reads (shotgun sequencing) against reference genomes
→ FastANI to compare (draft) genomes by Average Nucleotide Identity (ANI)
read more