BA10A 
Compute the Probability of a Hidden Path

249


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

206


BA10C 
Implement the Viterbi Algorithm

128


BA10D 
Compute the Probability of a String Emitted by an HMM

115


BA10E 
Construct a Profile HMM

82


BA10F 
Construct a Profile HMM with Pseudocounts

72


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

33


BA10H 
Estimate the Parameters of an HMM

47


BA10I 
Implement Viterbi Learning

37


BA10J 
Solve the Soft Decoding Problem

35


BA10K 
Implement BaumWelch Learning

26


BA11A 
Construct the Graph of a Spectrum

65


BA11B 
Implement DecodingIdealSpectrum

49


BA11C 
Convert a Peptide into a Peptide Vector

71


BA11D 
Convert a Peptide Vector into a Peptide

65


BA11E 
Sequence a Peptide

41


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

42


BA11G 
Implement PSMSearch

40


BA11H 
Compute the Size of a Spectral Dictionary

35


BA11I 
Compute the Probability of a Spectral Dictionary

34


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

26


BA1A 
Compute the Number of Times a Pattern Appears in a Text

498


BA1B 
Find the Most Frequent Words in a String

668


BA1C 
Find the Reverse Complement of a String

604


BA1D 
Find All Occurrences of a Pattern in a String

574


BA1E 
Find Patterns Forming Clumps in a String

460


BA1F 
Find a Position in a Genome Minimizing the Skew

437


BA1G 
Compute the Hamming Distance Between Two Strings

423


BA1H 
Find All Approximate Occurrences of a Pattern in a String

445


BA1I 
Find the Most Frequent Words with Mismatches in a String

350


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

317


BA1K 
Generate the Frequency Array of a String

279


BA1L 
Implement PatternToNumber

311


BA1M 
Implement NumberToPattern

282


BA1N 
Generate the dNeighborhood of a String

311


BA2A 
Implement MotifEnumeration

266


BA2B 
Find a Median String

227


BA2C 
Find a Profilemost Probable kmer in a String

243


BA2D 
Implement GreedyMotifSearch

198


BA2E 
Implement GreedyMotifSearch with Pseudocounts

165


BA2F 
Implement RandomizedMotifSearch

140


BA2G 
Implement GibbsSampler

129


BA2H 
Implement DistanceBetweenPatternAndStrings

165


BA3A 
Generate the kmer Composition of a String

275


BA3B 
Reconstruct a String from its Genome Path

223


BA3C 
Construct the Overlap Graph of a Collection of kmers

226


BA3D 
Construct the De Bruijn Graph of a String

215


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

195


BA3F 
Find an Eulerian Cycle in a Graph

148


BA3G 
Find an Eulerian Path in a Graph

136


BA3H 
Reconstruct a String from its kmer Composition

137


BA3I 
Find a kUniversal Circular String

113


BA3J 
Reconstruct a String from its Paired Composition

88


BA3K 
Generate Contigs from a Collection of Reads

98


BA3L 
Construct a String Spelled by a Gapped Genome Path

83


BA3M 
Generate All Maximal NonBranching Paths in a Graph

86


BA4A 
Translate an RNA String into an Amino Acid String

195


BA4B 
Find Substrings of a Genome Encoding a Given Amino Acid String

157


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

156


BA4D 
Compute the Number of Peptides of Given Total Mass

76


BA4E 
Find a Cyclic Peptide with Theoretical Spectrum Matching an Ideal Spectrum

107


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

94


BA4G 
Implement LeaderboardCyclopeptideSequencing

90


BA4H 
Generate the Convolution of a Spectrum

93


BA4I 
Implement ConvolutionCyclopeptideSequencing

63


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

97


BA4K 
Compute the Score of a Linear Peptide

81


BA4L 
Trim a Peptide Leaderboard

70


BA4M 
Solve the Turnpike Problem

41


BA5A 
Find the Minimum Number of Coins Needed to Make Change

358


BA5B 
Find the Length of a Longest Path in a Manhattanlike Grid

299


BA5C 
Find a Longest Common Subsequence of Two Strings

347


BA5D 
Find the Longest Path in a DAG

248


BA5E 
Find a HighestScoring Alignment of Two Strings

269


BA5F 
Find a HighestScoring Local Alignment of Two Strings

236


BA5G 
Compute the Edit Distance Between Two Strings

294


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

190


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

180


BA5J 
Align Two Strings Using Affine Gap Penalties

162


BA5K 
Find a Middle Edge in an Alignment Graph in Linear Space

121


BA5L 
Align Two Strings Using Linear Space

101


BA5M 
Find a HighestScoring Multiple Sequence Alignment

126


BA5N 
Find a Topological Ordering of a DAG

73


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

224


BA6B 
Compute the Number of Breakpoints in a Permutation

240


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

157


BA6D 
Find a Shortest Transformation of One Genome into Another by 2Breaks

33


BA6E 
Find All Shared kmers of a Pair of Strings

167


BA6F 
Implement ChromosomeToCycle

84


BA6G 
Implement CycleToChromosome

79


BA6H 
Implement ColoredEdges

74


BA6I 
Implement GraphToGenome

59


BA6J 
Implement 2BreakOnGenomeGraph

56


BA6K 
Implement 2BreakOnGenome

39


BA7A 
Compute Distances Between Leaves

95


BA7B 
Compute Limb Lengths in a Tree

89


BA7C 
Implement AdditivePhylogeny

59


BA7D 
Implement UPGMA

54


BA7E 
Implement the Neighbor Joining Algorithm

48


BA7F 
Implement SmallParsimony

40


BA7G 
Adapt SmallParsimony to Unrooted Trees

26


BA8A 
Implement FarthestFirstTraversal

66


BA8B 
Compute the Squared Error Distortion

64


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

61


BA8D 
Implement the Soft kMeans Clustering Algorithm

56


BA8E 
Implement Hierarchical Clustering

48


BA9A 
Construct a Trie from a Collection of Patterns

190


BA9B 
Implement TrieMatching

167


BA9C 
Construct the Suffix Tree of a String

129


BA9D 
Find the Longest Repeat in a String

145


BA9E 
Find the Longest Substring Shared by Two Strings

143


BA9F 
Find the Shortest NonShared Substring of Two Strings

112


BA9G 
Construct the Suffix Array of a String

147


BA9H 
Pattern Matching with the Suffix Array

69


BA9I 
Construct the BurrowsWheeler Transform of a String

170


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

142


BA9K 
Generate the LasttoFirst Mapping of a String

62


BA9L 
Implement BWMatching

107


BA9M 
Implement BetterBWMatching

102


BA9N 
Find All Occurrences of a Collection of Patterns in a String

114


BA9O 
Find All Approximate Occurrences of a Collection of Patterns in a String

87


BA9P 
Implement TreeColoring

38


BA9Q 
Construct the Partial Suffix Array of a String

88


BA9R 
Construct a Suffix Tree from a Suffix Array

65

