BA10A 
Compute the Probability of a Hidden Path

402


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

343


BA10C 
Implement the Viterbi Algorithm

206


BA10D 
Compute the Probability of a String Emitted by an HMM

182


BA10E 
Construct a Profile HMM

120


BA10F 
Construct a Profile HMM with Pseudocounts

111


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

56


BA10H 
Estimate the Parameters of an HMM

70


BA10I 
Implement Viterbi Learning

61


BA10J 
Solve the Soft Decoding Problem

61


BA10K 
Implement BaumWelch Learning

48


BA11A 
Construct the Graph of a Spectrum

97


BA11B 
Implement DecodingIdealSpectrum

68


BA11C 
Convert a Peptide into a Peptide Vector

100


BA11D 
Convert a Peptide Vector into a Peptide

94


BA11E 
Sequence a Peptide

56


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

57


BA11G 
Implement PSMSearch

56


BA11H 
Compute the Size of a Spectral Dictionary

47


BA11I 
Compute the Probability of a Spectral Dictionary

47


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

37


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

856


BA1B 
Find the Most Frequent Words in a String

1023


BA1C 
Find the Reverse Complement of a String

970


BA1D 
Find All Occurrences of a Pattern in a String

884


BA1E 
Find Patterns Forming Clumps in a String

679


BA1F 
Find a Position in a Genome Minimizing the Skew

666


BA1G 
Compute the Hamming Distance Between Two Strings

737


BA1H 
Find All Approximate Occurrences of a Pattern in a String

635


BA1I 
Find the Most Frequent Words with Mismatches in a String

509


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

457


BA1K 
Generate the Frequency Array of a String

423


BA1L 
Implement PatternToNumber

476


BA1M 
Implement NumberToPattern

439


BA1N 
Generate the dNeighborhood of a String

464


BA2A 
Implement MotifEnumeration

377


BA2B 
Find a Median String

369


BA2C 
Find a Profilemost Probable kmer in a String

388


BA2D 
Implement GreedyMotifSearch

320


BA2E 
Implement GreedyMotifSearch with Pseudocounts

268


BA2F 
Implement RandomizedMotifSearch

222


BA2G 
Implement GibbsSampler

204


BA2H 
Implement DistanceBetweenPatternAndStrings

253


BA3A 
Generate the kmer Composition of a String

464


BA3B 
Reconstruct a String from its Genome Path

431


BA3C 
Construct the Overlap Graph of a Collection of kmers

377


BA3D 
Construct the De Bruijn Graph of a String

392


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

369


BA3F 
Find an Eulerian Cycle in a Graph

271


BA3G 
Find an Eulerian Path in a Graph

228


BA3H 
Reconstruct a String from its kmer Composition

217


BA3I 
Find a kUniversal Circular String

165


BA3J 
Reconstruct a String from its Paired Composition

158


BA3K 
Generate Contigs from a Collection of Reads

159


BA3L 
Construct a String Spelled by a Gapped Genome Path

134


BA3M 
Generate All Maximal NonBranching Paths in a Graph

111


BA4A 
Translate an RNA String into an Amino Acid String

323


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

229


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

228


BA4D 
Compute the Number of Peptides of Given Total Mass

123


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

158


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

130


BA4G 
Implement LeaderboardCyclopeptideSequencing

121


BA4H 
Generate the Convolution of a Spectrum

123


BA4I 
Implement ConvolutionCyclopeptideSequencing

90


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

143


BA4K 
Compute the Score of a Linear Peptide

108


BA4L 
Trim a Peptide Leaderboard

94


BA4M 
Solve the Turnpike Problem

63


BA5A 
Find the Minimum Number of Coins Needed to Make Change

445


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

358


BA5C 
Find a Longest Common Subsequence of Two Strings

445


BA5D 
Find the Longest Path in a DAG

293


BA5E 
Find a HighestScoring Alignment of Two Strings

399


BA5F 
Find a HighestScoring Local Alignment of Two Strings

330


BA5G 
Compute the Edit Distance Between Two Strings

404


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

251


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

230


BA5J 
Align Two Strings Using Affine Gap Penalties

248


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

164


BA5L 
Align Two Strings Using Linear Space

143


BA5M 
Find a HighestScoring Multiple Sequence Alignment

167


BA5N 
Find a Topological Ordering of a DAG

105


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

263


BA6B 
Compute the Number of Breakpoints in a Permutation

287


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

184


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

55


BA6E 
Find All Shared kmers of a Pair of Strings

197


BA6F 
Implement ChromosomeToCycle

113


BA6G 
Implement CycleToChromosome

108


BA6H 
Implement ColoredEdges

98


BA6I 
Implement GraphToGenome

81


BA6J 
Implement 2BreakOnGenomeGraph

74


BA6K 
Implement 2BreakOnGenome

64


BA7A 
Compute Distances Between Leaves

124


BA7B 
Compute Limb Lengths in a Tree

128


BA7C 
Implement AdditivePhylogeny

88


BA7D 
Implement UPGMA

84


BA7E 
Implement the Neighbor Joining Algorithm

70


BA7F 
Implement SmallParsimony

63


BA7G 
Adapt SmallParsimony to Unrooted Trees

40


BA8A 
Implement FarthestFirstTraversal

96


BA8B 
Compute the Squared Error Distortion

92


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

95


BA8D 
Implement the Soft kMeans Clustering Algorithm

79


BA8E 
Implement Hierarchical Clustering

75


BA9A 
Construct a Trie from a Collection of Patterns

223


BA9B 
Implement TrieMatching

200


BA9C 
Construct the Suffix Tree of a String

158


BA9D 
Find the Longest Repeat in a String

184


BA9E 
Find the Longest Substring Shared by Two Strings

172


BA9F 
Find the Shortest NonShared Substring of Two Strings

138


BA9G 
Construct the Suffix Array of a String

183


BA9H 
Pattern Matching with the Suffix Array

98


BA9I 
Construct the BurrowsWheeler Transform of a String

216


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

178


BA9K 
Generate the LasttoFirst Mapping of a String

102


BA9L 
Implement BWMatching

138


BA9M 
Implement BetterBWMatching

124


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

137


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

109


BA9P 
Implement TreeColoring

53


BA9Q 
Construct the Partial Suffix Array of a String

111


BA9R 
Construct a Suffix Tree from a Suffix Array

83

