arkhan19 / beng-181

Bioinformatics Algorithms

Beng-181

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