├── README.md ├── week1-2 ├── 1-Clump Finding Problem.py ├── 2-Minimum Skew Problem.py ├── 3-Approximate Pattern Matching Problem.py ├── 4-Frequent Words with Mismatches Problem(new).py ├── 4-Frequent Words with Mismatches Problem.py ├── 5-Reverse Complements Problem.py ├── approximate_match.txt ├── clump_finding.txt ├── frequent_words_mismatch.txt ├── frequent_words_mismatch_complements.txt ├── minimum_skew.txt └── rosalind_ba1e.txt ├── week11-12 ├── 26 - Implement GreedySorting to Sort a Permutation by Reversals.py ├── 26.py ├── 27.py ├── 28.py ├── 29.py ├── 2BreakDistance.txt ├── 2BreakOnGenome.txt ├── 2BreakSorting.txt ├── 30.py ├── GreedySorting.txt ├── NumberOfBreakpoints.txt └── test.py ├── week3-4 ├── 10-Implement DistanceBetweenPatternAndStrings.py ├── 6-Implement GreedyMotifSearch.py ├── 7-Implement GreedyMotifSearch with Pseudocounts.py ├── 8-Implement RandomizedMotifSearch.py ├── 9-Implement GibbsSampler.py ├── distance_between_pattern_and_strings.txt ├── gibbs.txt ├── greedy_motif_search.txt ├── greedy_motif_search_pseudocounts.txt ├── output_BA2F.txt └── randomized_motif_search.txt ├── week5-6 ├── 11 - String Reconstruction Problem.py ├── 111.py ├── 12 - k-Universal Circular String Problem.py ├── 123.py ├── 13 - String Reconstruction from Read-Pairs Problem.py ├── 14 - Contig Generation Problem.py ├── 15 - Gapped Genome Path String Problem.py ├── StringReconstructionProblem.txt ├── contig_generation.txt ├── help.py ├── string_reconstruction_from_read_pairs.txt ├── string_spelled_by_gapped_patterns (2).txt └── universal_string.txt ├── week7-8 ├── 16 - Find Substrings of a Genome Encoding a Given Amino Acid String.py ├── 17 - Compute the Number of Peptides of Given Total Mass.py ├── 18 - Cyclopeptide Sequencing1.py ├── 19 - LeaderboardCyclopeptideSequencing.py ├── 20 - ConvolutionCyclopeptideSequencing.py ├── codon_table.txt ├── convolution_cyclopeptide_sequencing.txt ├── counting_peptides.txt ├── cyclopeptide_sequencing.txt ├── data.txt ├── integer_mass_table.txt ├── leaderboard_cyclopeptide_sequencing.txt ├── peptide_encoding.txt └── test_dataset.txt └── week9-10 ├── 21 - The Change Problem.py ├── 22 - Manhattan Tourist Problem.py ├── 23 - Global_Alignment_Problem.py ├── 24 - Local_Alignment_Problem.py ├── 25 - Global_Alignment_in_Linear_Space_Problem.py ├── BLOSUM62.txt ├── Manhattan_tourist.txt ├── PAM250.txt ├── change_problem.txt ├── global_alignment.txt ├── linear_space_alignment.txt └── local_alignment.txt /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Butskov/Bioinformatics-Algorithms/HEAD/README.md -------------------------------------------------------------------------------- /week1-2/1-Clump Finding Problem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Butskov/Bioinformatics-Algorithms/HEAD/week1-2/1-Clump Finding Problem.py 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