BA10A 
Compute the Probability of a Hidden Path

257


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

217


BA10C 
Implement the Viterbi Algorithm

132


BA10D 
Compute the Probability of a String Emitted by an HMM

119


BA10E 
Construct a Profile HMM

84


BA10F 
Construct a Profile HMM with Pseudocounts

74


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

33


BA10H 
Estimate the Parameters of an HMM

49


BA10I 
Implement Viterbi Learning

39


BA10J 
Solve the Soft Decoding Problem

38


BA10K 
Implement BaumWelch Learning

29


BA11A 
Construct the Graph of a Spectrum

67


BA11B 
Implement DecodingIdealSpectrum

50


BA11C 
Convert a Peptide into a Peptide Vector

73


BA11D 
Convert a Peptide Vector into a Peptide

67


BA11E 
Sequence a Peptide

42


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

43


BA11G 
Implement PSMSearch

41


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

517


BA1B 
Find the Most Frequent Words in a String

700


BA1C 
Find the Reverse Complement of a String

624


BA1D 
Find All Occurrences of a Pattern in a String

590


BA1E 
Find Patterns Forming Clumps in a String

472


BA1F 
Find a Position in a Genome Minimizing the Skew

455


BA1G 
Compute the Hamming Distance Between Two Strings

438


BA1H 
Find All Approximate Occurrences of a Pattern in a String

456


BA1I 
Find the Most Frequent Words with Mismatches in a String

358


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

326


BA1K 
Generate the Frequency Array of a String

287


BA1L 
Implement PatternToNumber

323


BA1M 
Implement NumberToPattern

290


BA1N 
Generate the dNeighborhood of a String

320


BA2A 
Implement MotifEnumeration

270


BA2B 
Find a Median String

232


BA2C 
Find a Profilemost Probable kmer in a String

247


BA2D 
Implement GreedyMotifSearch

199


BA2E 
Implement GreedyMotifSearch with Pseudocounts

167


BA2F 
Implement RandomizedMotifSearch

142


BA2G 
Implement GibbsSampler

131


BA2H 
Implement DistanceBetweenPatternAndStrings

165


BA3A 
Generate the kmer Composition of a String

286


BA3B 
Reconstruct a String from its Genome Path

231


BA3C 
Construct the Overlap Graph of a Collection of kmers

231


BA3D 
Construct the De Bruijn Graph of a String

220


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

202


BA3F 
Find an Eulerian Cycle in a Graph

153


BA3G 
Find an Eulerian Path in a Graph

142


BA3H 
Reconstruct a String from its kmer Composition

145


BA3I 
Find a kUniversal Circular String

117


BA3J 
Reconstruct a String from its Paired Composition

92


BA3K 
Generate Contigs from a Collection of Reads

105


BA3L 
Construct a String Spelled by a Gapped Genome Path

85


BA3M 
Generate All Maximal NonBranching Paths in a Graph

86


BA4A 
Translate an RNA String into an Amino Acid String

203


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

161


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

162


BA4D 
Compute the Number of Peptides of Given Total Mass

79


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

108


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

94


BA4G 
Implement LeaderboardCyclopeptideSequencing

91


BA4H 
Generate the Convolution of a Spectrum

94


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

71


BA4M 
Solve the Turnpike Problem

43


BA5A 
Find the Minimum Number of Coins Needed to Make Change

365


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

306


BA5C 
Find a Longest Common Subsequence of Two Strings

363


BA5D 
Find the Longest Path in a DAG

253


BA5E 
Find a HighestScoring Alignment of Two Strings

280


BA5F 
Find a HighestScoring Local Alignment of Two Strings

244


BA5G 
Compute the Edit Distance Between Two Strings

308


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

204


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

186


BA5J 
Align Two Strings Using Affine Gap Penalties

172


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

122


BA5L 
Align Two Strings Using Linear Space

102


BA5M 
Find a HighestScoring Multiple Sequence Alignment

127


BA5N 
Find a Topological Ordering of a DAG

74


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

225


BA6B 
Compute the Number of Breakpoints in a Permutation

243


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

158


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

88


BA6G 
Implement CycleToChromosome

83


BA6H 
Implement ColoredEdges

77


BA6I 
Implement GraphToGenome

61


BA6J 
Implement 2BreakOnGenomeGraph

57


BA6K 
Implement 2BreakOnGenome

41


BA7A 
Compute Distances Between Leaves

97


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

41


BA7G 
Adapt SmallParsimony to Unrooted Trees

26


BA8A 
Implement FarthestFirstTraversal

69


BA8B 
Compute the Squared Error Distortion

68


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

64


BA8D 
Implement the Soft kMeans Clustering Algorithm

58


BA8E 
Implement Hierarchical Clustering

50


BA9A 
Construct a Trie from a Collection of Patterns

191


BA9B 
Implement TrieMatching

168


BA9C 
Construct the Suffix Tree of a String

130


BA9D 
Find the Longest Repeat in a String

147


BA9E 
Find the Longest Substring Shared by Two Strings

145


BA9F 
Find the Shortest NonShared Substring of Two Strings

114


BA9G 
Construct the Suffix Array of a String

148


BA9H 
Pattern Matching with the Suffix Array

71


BA9I 
Construct the BurrowsWheeler Transform of a String

171


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

143


BA9K 
Generate the LasttoFirst Mapping of a String

63


BA9L 
Implement BWMatching

110


BA9M 
Implement BetterBWMatching

104


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

115


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

88


BA9P 
Implement TreeColoring

38


BA9Q 
Construct the Partial Suffix Array of a String

92


BA9R 
Construct a Suffix Tree from a Suffix Array

66

