Bioinformatics Algorithms
Use of python programming in order to execute key bioinformatics algorithms
Problems based of the book written by Pavel Penzner and Phillip Compeau http://bioinformaticsalgorithms.com/index.htm
1 Compute the Number of Times a Pattern Appears in a Text
2 Find the Most Frequent Words in a String
3 Find the Reverse Complement of a String
4 Find All Occurrences of a Pattern in a String
5 Find Patterns Forming Clumps in a String
6 Find a Position in a Genome Minimizing the Skew
7 Compute the Hamming Distance Between Two Strings
8 Find All Approximate Occurrences of a Pattern in a String
9 Find the Most Frequent Words with Mismatches in a String
10 Find Frequent Words with Mismatches and Reverse Complements
11 Generate the Frequency Array of a String
12 Implement PatternToNumber
13 Implement NumberToPattern
14 Generate the d-Neighborhood of a String
15 Implement MotifEnumeration
16 Find a Median String
17 Find a Profile-most Probable k-mer in a String
18 Implement GreedyMotifSearch
19 Implement GreedyMotifSearch with Pseudocounts
20 Implement RandomizedMotifSearch
21 Implement GibbsSampler
22 Implement DistanceBetweenPatternAndStrings
23 Generate the k-mer Composition of a String
24 Reconstruct a String from its Genome Path
25 Construct the Overlap Graph of a Collection of k-mers
26 Construct the De Bruijn Graph of a String
27 Construct the De Bruijn Graph of a Collection of k-mers
28 Find an Eulerian Cycle in a Graph
29 Find an Eulerian Path in a Graph
30 Reconstruct a String from its k-mer Composition
31 Find a k-Universal Circular String
32 Reconstruct a String from its Paired Composition
33 Generate Contigs from a Collection of Reads
34 Construct a String Spelled by a Gapped Genome Path
35 Generate All Maximal Non-Branching Paths in a Graph
36 Find the Minimum Number of Coins Needed to Make Change
37 Find the Length of a Longest Path in a Manhattan-like Grid
38 Find a Longest Common Subsequence of Two Strings
39 Find the Longest Path in a DAG
40 Find a Highest-Scoring Alignment of Two Strings
41 Find a Highest-Scoring Local Alignment of Two Strings
42 Compute the Edit Distance Between Two Strings
43 Find a Highest-Scoring Fitting Alignment of Two Strings
44 Find a Highest-Scoring Overlap Alignment of Two Strings
45 Align Two Strings Using Affine Gap Penalties
46 Find a Middle Edge in an Alignment Graph in Linear Space
47 Align Two Strings Using Linear Space
48 Find a Highest-Scoring Multiple Sequence Alignment
49 Find a Topological Ordering of a DAG
50 Implement GreedySorting to Sort a Permutation by Reversals
51 Compute the Number of Breakpoints in a Permutation
52 Compute the 2-Break Distance Between a Pair of Genomes
53 Find a Shortest Transformation of One Genome into Another by 2-Breaks
54 Find All Shared k-mers of a Pair of Strings
55 Implement ChromosomeToCycle
56 Implement CycleToChromosome
57 Implement ColoredEdges
58 Implement GraphToGenome
59 Implement 2-BreakOnGenomeGraph
60 Implement 2-BreakOnGenome
61 Construct a Trie from a Collection of Patterns
62 Implement TrieMatching
63 Construct the Suffix Tree of a String
64 Find the Longest Repeat in a String
65 Find the Longest Substring Shared by Two Strings
66 Find the Shortest Non-Shared Substring of Two Strings
67 Construct the Suffix Array of a String
68 Pattern Matching with the Suffix Array
69 Construct the Burrows-Wheeler Transform of a String
70 Reconstruct a String from its Burrows-Wheeler Transform
71 Generate the Last-to-First Mapping of a String
72 Implement BWMatching
73 Implement BetterBWMatching
74 Find All Occurrences of a Collection of Patterns in a String