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run_example.txt
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Protein test, example from the labs:
./blast.sh -e ./data/scoring_matrix/blosum62.csv -d ./data/database/test.fa -k 3 -t 15 -q IHNWALN --delimiter ';'
Find hemoglobin in chromosome 16:
./blast.sh -e ./data/scoring_matrix/BLAST.csv -d ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa -k 8 -t 40 -q actcttctggtccccacagactcagagagaacccaccatggtgctgtctcctgccgacaagaccaacgtcaaggccgcctggggtaaggtcggcgcgcacgctggcgagtatggtgcggaggccctggagaggtgaggctccctcccctgctccgacccgggctcctcgcccgcccggacccacaggccaccctcaaccgtcctggccccggacccaaaccccacccctcactctgcttctccccgcaggatgttcctgtccttccccaccaccaagacctacttcccgcacttcgacctgagccacggctctgcccaggttaagggccacggcaagaaggtggccgacgcgctgaccaacgccgtggcgcacgtggacgacatgcccaacgcgctgtccgccctgagcgacctgcacgcgcacaagcttcgggtggacccggtcaacttcaaggtgagcggcgggccgggagcgatctgggtcgaggggcgagatggcgccttcctcgcagggcagaggatcacgcgggttgcgggaggtgtagcgcaggcggcggctgcgggcctgggccctcggccccactgaccctcttctctgcacagctcctaagccactgcctgctggtgaccctggccgcccacctccccgccgagttcacccctgcggtgcacgcctccctggacaagttcctggcttctgtgagcaccgtgctgacctccaaataccgttaagctggagcctcggtggccatgcttcttgccccttgggcctccccccagcccctcctccccttcctgcacccgtacccccgtggtctttgaataaagtctgagtgggcggca
Find hemoglobin in chromosomes 16, 17, 18, 19, 20:
./blast.sh -e ./data/scoring_matrix/BLAST.csv -d ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.17.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.18.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.20.fa -k 8 -t 40 -q actcttctggtccccacagactcagagagaacccaccatggtgctgtctcctgccgacaagaccaacgtcaaggccgcctggggtaaggtcggcgcgcacgctggcgagtatggtgcggaggccctggagaggtgaggctccctcccctgctccgacccgggctcctcgcccgcccggacccacaggccaccctcaaccgtcctggccccggacccaaaccccacccctcactctgcttctccccgcaggatgttcctgtccttccccaccaccaagacctacttcccgcacttcgacctgagccacggctctgcccaggttaagggccacggcaagaaggtggccgacgcgctgaccaacgccgtggcgcacgtggacgacatgcccaacgcgctgtccgccctgagcgacctgcacgcgcacaagcttcgggtggacccggtcaacttcaaggtgagcggcgggccgggagcgatctgggtcgaggggcgagatggcgccttcctcgcagggcagaggatcacgcgggttgcgggaggtgtagcgcaggcggcggctgcgggcctgggccctcggccccactgaccctcttctctgcacagctcctaagccactgcctgctggtgaccctggccgcccacctccccgccgagttcacccctgcggtgcacgcctccctggacaagttcctggcttctgtgagcaccgtgctgacctccaaataccgttaagctggagcctcggtggccatgcttcttgccccttgggcctccccccagcccctcctccccttcctgcacccgtacccccgtggtctttgaataaagtctgagtgggcggca
Find hemoglobin in human genome:
./blast.sh -e ./data/scoring_matrix/BLAST.csv -d ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.3.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.4.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.5.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.6.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.7.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.8.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.9.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.10.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.11.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.12.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.13.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.14.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.15.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.17.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.18.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.20.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.21.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.MT.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.X.fa ./data/database/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa -k 8 -t 40 -q actcttctggtccccacagactcagagagaacccaccatggtgctgtctcctgccgacaagaccaacgtcaaggccgcctggggtaaggtcggcgcgcacgctggcgagtatggtgcggaggccctggagaggtgaggctccctcccctgctccgacccgggctcctcgcccgcccggacccacaggccaccctcaaccgtcctggccccggacccaaaccccacccctcactctgcttctccccgcaggatgttcctgtccttccccaccaccaagacctacttcccgcacttcgacctgagccacggctctgcccaggttaagggccacggcaagaaggtggccgacgcgctgaccaacgccgtggcgcacgtggacgacatgcccaacgcgctgtccgccctgagcgacctgcacgcgcacaagcttcgggtggacccggtcaacttcaaggtgagcggcgggccgggagcgatctgggtcgaggggcgagatggcgccttcctcgcagggcagaggatcacgcgggttgcgggaggtgtagcgcaggcggcggctgcgggcctgggccctcggccccactgaccctcttctctgcacagctcctaagccactgcctgctggtgaccctggccgcccacctccccgccgagttcacccctgcggtgcacgcctccctggacaagttcctggcttctgtgagcaccgtgctgacctccaaataccgttaagctggagcctcggtggccatgcttcttgccccttgggcctccccccagcccctcctccccttcctgcacccgtacccccgtggtctttgaataaagtctgagtgggcggca