├── Chapter10 ├── DeterministicMotifFinding.py ├── MySeq.py └── exampleMotifs.txt ├── Chapter11 ├── MotifFinding.py ├── MyMotifs.py ├── MySeq.py ├── __pycache__ │ ├── MyMotifs.cpython-36.pyc │ └── MySeq.cpython-36.pyc ├── exampleMotifs.txt ├── motifs_biopython.py └── mymotif.png ├── Chapter12 └── HiddenMarkovModel.py ├── Chapter13 └── MyGraph.py ├── Chapter14 ├── MetabolicNetwork.py └── MyGraph.py ├── Chapter15 ├── MyGraph.py ├── assembly_ch15.py └── debruijn_ch15.py ├── Chapter16 ├── BWT.py ├── SuffixTree.py └── Trie.py ├── Chapter2 ├── MySeq.py ├── NumMatrix_ch2_proj3.py ├── exs_ch2_3a.py ├── exs_ch2_3b.py ├── exs_ch2_3c.py ├── exs_ch2_3e.py ├── exs_ch2_3f.py ├── exs_ch2_3g.py ├── exs_ch2_3h.py ├── exs_ch2_3i.py ├── exs_ch2_3j.py ├── exs_ch2_4a.py ├── exs_ch2_4b.py ├── exs_ch2_4d.py ├── exs_ch2_4e.py ├── exs_ch2_4h.py ├── exs_ch2_4i.py ├── exs_ch2_4j.py ├── frequencies.py └── rectangle_ex5.py ├── Chapter4 ├── MySeq-ch4.py ├── NC_005816.fna ├── NC_005816.gb ├── biopython_examples_ch4.py ├── exs_ch4_1.py ├── exs_ch4_3.py ├── exs_ch4_4.py ├── exs_ch4_6.py ├── exs_ch4_7.py ├── ls_orchid.gbk └── seqs_ch4.py ├── Chapter5 ├── Automata_ch5.py ├── BoyerMoore_ch5.py ├── NC_005816.fna ├── exs_ch5_1.py ├── exs_ch5_4.py ├── exs_ch5_5.py ├── exs_ch5_6.py ├── exuniprot.fasta ├── functionsRE-ch5.py ├── naive_funcs_ch5.py ├── prosite_ch5.py ├── restriction_ch5.py └── seqs_ch5.py ├── Chapter6 ├── Proj_ch6_1 │ ├── MyAlign.py │ ├── PairwiseAlignment.py │ └── SubstMatrix.py ├── align_ch6.py ├── blosum62.mat ├── dotplots.py ├── exs_ch6_1.pdf ├── exs_ch6_3.py ├── exs_ch6_4and5.py └── pairwise_ch6.py ├── Chapter7 ├── O14727.fasta ├── biopython_blast_dna.py ├── biopython_blast_prot.py ├── example_blast.fasta ├── exs_ch7_3.py ├── interl10.fasta ├── myblast_ch7.py └── seqBlast.txt ├── Chapter8 ├── MultipleAlignment.py ├── MyAlign.py ├── MySeq.py ├── PF05371_seed.aln ├── PairwiseAlignment.py ├── SubstMatrix.py ├── align-ficha10_2.clustal ├── biopython_align_ch8.py ├── 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