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Posted on Sep 22, 2024

Using Python Calculate the Jaccard index between the genomes, for k- (4, 8, 12). Do this for unique mers and accounting for mer frequency 4.

image text in transcribed Using Python

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Calculate the Jaccard index between the genomes, for k- (4, 8, 12). Do this for unique mers and accounting for mer frequency 4. fasta 1.fasta NC 003997.3 Bacillus anthracis str. Ames chromosome, complete genome ATATTTTTTCTTGTTTTTTATATCCACAAACTCTTTTCGTACTTTTACACAGTATATCGTGTTGTGGACA ATTTTATTCCACAAGGTATTGATTTTGTGGATAACTTTCTTAATTTCATTGCTATAGCTACTTTTTTTTG ATATTATAGTTGTGTTTTCACTTTGAATAAGTTTTC CAC ATC CACAATTTGTGTATAAC ATGTGGACAGTTTTAATCACATGTGGGTAAATGATTATCCACATTTGCTTTTTTGTCGAAAACCCTATCT CATATACAAACGACGTTTTTAGGTTTTAAAATACGTTTCGTATAAATATACATTTTATATTTATTCAGGT TGTACATTTGTTGCACAACCTTATTCTTTTACCATCTTAGTAAAGGAGGGACACCTTTGGAAAACATCTO TGATTTATGGAACAGCGCCTTAAAAGAACTCGAAAAAAAGGTCAGTAAACCAAGTTATGAAACATGGTTA AAATCAACAACCGCACATAATTTAAAGAAAGATGTATTAACAATTACGGCTCCAAATGAATTCGCCCGTG ATTGGTTAGAATCTCATTATTCAGAGCTAATTTCGGAAACACTTTATGATTTAACGGGGGCAAAATTAGC TATTCGCTTTATTATTCCCCAAAGTCAAGCTGAAGAGGAGATTGATCTTCCTCCTGCTAAACCAAATGCA GCACAAGATGATTCTAATCATTTACCACAGAGTATGCTAAACCCAAAATATACGTTTGATACATTTGTTA TTGGCTCTGGTAACCGTTTTGCTCACGCTGCTTCATTGGCCGTAGCCGAAGCGCCAGCTAAAGCATATAA TCCCCTCTTTATTTATGGGGGAGTTGGACTTGGAAAAACCCATTTAATGCATGCAATTGGCCATTATGTA ATTGAACATAACCCAAATGCCAAAGTTGTATATTTATCATCAGAAAAATTTACAAATGAATTCATTAATT GTGATAATAAAG CGGTC GATTTTCGTAATAAATACC GCAATGTAGATGTTTTATTGATAGATGA TATTCAATTTTTAGCGGGAAAAGAACAAACTCAAGAAGAGTTTTTCCATACATTCAATGCATTACACGAA GAAAGTAAACAAATTGTAATTTCCAGTGATCGGCCACCAAAAGAAATTCCAACTTTAGAAGATCGTCTTC GTTCTCGCTTTGAATGGGGACTCATTACGGATATTACGCCACCAGATTTAGAAACACGAATTGCGATTTT ACGTAAAAAGGCAAAGGCTGAAGGACTTGATATACCAAATGAGGTCATGCTTTATATCGCAAATCAAATC GATTCAAATATTCGTGAACTAGAAGGTGCACTCATCCGCGTTGTAGCTTATTCATCTTTAATTAACAAGG ATATTAATGCTGATTTAGCAGCTGAAGCACTTAAAGATATTATTCCAAATTCTAAACCAAAAATTATCTO CATTTATGATATTCAAAAAGCTGTTGGAGATGTTTATCAAGTAAAATTAGAAGATTTCAAGGCGAAAAAG CGCACAAAGTCAGTTGCCTTTCCTCGCCAAATTGCAATGTATTTGTCACGCGAACTGACAGATTCCTCCT TACCTAAAATAGGTGAAGAATTTGGTGGACGTGATCATACAACCGTTATCCATGCCCATGAAAAAATTTC TAAGCTACTTAAGACGGATACGCAATTACAAAAACAAGTTGAAGAAATTAACGATATTTTAAAGTAGTAG CTGAATAGTGTGAATAACTTCCCTTGTTTTACGCACAGTCTATCCACATGTAGATAGACTGTTTTTACAT GGGGTTATC CAC ATATC CAC AAGCCCTATTAC TATTAC TAC TATTTTTTATCTTTATTAATT AATAAAATCTTATACTTACCGGAGGTTCTTCTTTATGCGTTTTTCAATTCAAAAAGACTATCTTGTAAG AAGTGTACAAGATGTAATGAAGGCTGTTTCTTTTCGTACAACAATTCCGATCCTTACAGGAATTAAAGTT Calculate the Jaccard index between the genomes, for k- (4, 8, 12). Do this for unique mers and accounting for mer frequency 4. fasta 1.fasta NC 003997.3 Bacillus anthracis str. Ames chromosome, complete genome ATATTTTTTCTTGTTTTTTATATCCACAAACTCTTTTCGTACTTTTACACAGTATATCGTGTTGTGGACA ATTTTATTCCACAAGGTATTGATTTTGTGGATAACTTTCTTAATTTCATTGCTATAGCTACTTTTTTTTG ATATTATAGTTGTGTTTTCACTTTGAATAAGTTTTC CAC ATC CACAATTTGTGTATAAC ATGTGGACAGTTTTAATCACATGTGGGTAAATGATTATCCACATTTGCTTTTTTGTCGAAAACCCTATCT CATATACAAACGACGTTTTTAGGTTTTAAAATACGTTTCGTATAAATATACATTTTATATTTATTCAGGT TGTACATTTGTTGCACAACCTTATTCTTTTACCATCTTAGTAAAGGAGGGACACCTTTGGAAAACATCTO TGATTTATGGAACAGCGCCTTAAAAGAACTCGAAAAAAAGGTCAGTAAACCAAGTTATGAAACATGGTTA AAATCAACAACCGCACATAATTTAAAGAAAGATGTATTAACAATTACGGCTCCAAATGAATTCGCCCGTG ATTGGTTAGAATCTCATTATTCAGAGCTAATTTCGGAAACACTTTATGATTTAACGGGGGCAAAATTAGC TATTCGCTTTATTATTCCCCAAAGTCAAGCTGAAGAGGAGATTGATCTTCCTCCTGCTAAACCAAATGCA GCACAAGATGATTCTAATCATTTACCACAGAGTATGCTAAACCCAAAATATACGTTTGATACATTTGTTA TTGGCTCTGGTAACCGTTTTGCTCACGCTGCTTCATTGGCCGTAGCCGAAGCGCCAGCTAAAGCATATAA TCCCCTCTTTATTTATGGGGGAGTTGGACTTGGAAAAACCCATTTAATGCATGCAATTGGCCATTATGTA ATTGAACATAACCCAAATGCCAAAGTTGTATATTTATCATCAGAAAAATTTACAAATGAATTCATTAATT GTGATAATAAAG CGGTC GATTTTCGTAATAAATACC GCAATGTAGATGTTTTATTGATAGATGA TATTCAATTTTTAGCGGGAAAAGAACAAACTCAAGAAGAGTTTTTCCATACATTCAATGCATTACACGAA GAAAGTAAACAAATTGTAATTTCCAGTGATCGGCCACCAAAAGAAATTCCAACTTTAGAAGATCGTCTTC GTTCTCGCTTTGAATGGGGACTCATTACGGATATTACGCCACCAGATTTAGAAACACGAATTGCGATTTT ACGTAAAAAGGCAAAGGCTGAAGGACTTGATATACCAAATGAGGTCATGCTTTATATCGCAAATCAAATC GATTCAAATATTCGTGAACTAGAAGGTGCACTCATCCGCGTTGTAGCTTATTCATCTTTAATTAACAAGG ATATTAATGCTGATTTAGCAGCTGAAGCACTTAAAGATATTATTCCAAATTCTAAACCAAAAATTATCTO CATTTATGATATTCAAAAAGCTGTTGGAGATGTTTATCAAGTAAAATTAGAAGATTTCAAGGCGAAAAAG CGCACAAAGTCAGTTGCCTTTCCTCGCCAAATTGCAATGTATTTGTCACGCGAACTGACAGATTCCTCCT TACCTAAAATAGGTGAAGAATTTGGTGGACGTGATCATACAACCGTTATCCATGCCCATGAAAAAATTTC TAAGCTACTTAAGACGGATACGCAATTACAAAAACAAGTTGAAGAAATTAACGATATTTTAAAGTAGTAG CTGAATAGTGTGAATAACTTCCCTTGTTTTACGCACAGTCTATCCACATGTAGATAGACTGTTTTTACAT GGGGTTATC CAC ATATC CAC AAGCCCTATTAC TATTAC TAC TATTTTTTATCTTTATTAATT AATAAAATCTTATACTTACCGGAGGTTCTTCTTTATGCGTTTTTCAATTCAAAAAGACTATCTTGTAAG AAGTGTACAAGATGTAATGAAGGCTGTTTCTTTTCGTACAACAATTCCGATCCTTACAGGAATTAAAGTT