Part A
./makeblastdb -in /Users/Emma/Documents/bioinfo_assignment_1/uniprot_sprot_010913.fasta -dbtype prot -out /Users/Emma/Documents/bioinfo_assignment_1/uniprot_db_010913

./blastx -num_threads 8 -out /Users/Emma/Documents/bioinfo_assignment_1/blastx_output -db /Users/Emma/Documents/bioinfo_assignment_1/uniprot_db_010913  -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -query /Users/Emma/Documents/bioinfo_assignment_1/Unknown_Transcriptome_31545_contigs.fa.txt 

Part B

./makeblastdb -in /Users/Emma/Documents/bioinfo_assignment_1/Unknown_Transcriptome_31545_contigs.fa.txt -dbtype nucl -out /Users/Emma/Documents/bioinfo_assignment_1/Nucleotide_database_for_Part_B 

./tblastn -num_threads 8 -out /Users/Emma/Documents/bioinfo_assignment_1/protamine_seq_orthologs -db /Users/Emma/Documents/bioinfo_assignment_1/Nucleotide_database_for_Part_B -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -query /Users/Emma/Documents/bioinfo_assignment_1/protamine_sequences.fasta.txt 

./makeblastdb -in /Users/Emma/Documents/bioinfo_assignment_1/transeq_on_unknown_transcriptome_31545.fasta -dbtype prot -out /Users/Emma/Documents/bioinfo_assignment_1/Protein_database_for_Part_B

./blastp -num_threads 8 -out /Users/Emma/Documents/bioinfo_assignment_1/protamine_seq_orthologs -db /Users/Emma/Documents/bioinfo_assignment_1/Protein_database_for_Part_B -outfmt 6 -evalue 1000 -max_target_seqs 1 -query /Users/Emma/Documents/bioinfo_assignment_1/protamine_sequences.fasta.txt