#Create a BLAST database from local sequences 

makeblastdb -in "Genome1.fna Genome2.fna" -out db_name -dbtype nucl -title "Database title" -parse_seqids -logfile logfile_name

#Combine BLAST databases

blastdb_aliastool -dblist "db1 db2" -dbtype nucl -out db_name -title "Database title" -logfile logfile_aliastool

#Submit BLASTN or BLASTX homology searches

blastn -query contigs.fasta -db db_name -num_descriptions 5 -num_alignments 5 -evalue 1e-50 -out blastn_results.txt -num_threads 6

blastx -query contigs.fasta -db db_name -num_descriptions 5 -num_alignments 5 -evalue 1e-17 -out blastx_results.txt -num_threads 6