BLAST+ Commands

 makeblastdb -in pdbaa.fasta -title pdbaa -dbtype prot -out pdbaa -parse_seqids

 blastp -query proteins.fasta -db db/pdbaa -out proteins_blastp.txt

 blastn

Legacy BLAST commands

 formatdb -i genome.fasta -p [F,T] -o T

 blastall -p [blastn, blastp, tblastn, blastx] -d genome.fasta -i seq.fasta -o out -

References

https://www.biostars.org/p/1557/

http://evomics.org/learning/bioinformatics/blast-laboratory/

http://computing.bio.cam.ac.uk/local/doc/blast+_user_manual.pdf