BA10A 
Compute the Probability of a Hidden Path

299


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

250


BA10C 
Implement the Viterbi Algorithm

153


BA10D 
Compute the Probability of a String Emitted by an HMM

137


BA10E 
Construct a Profile HMM

90


BA10F 
Construct a Profile HMM with Pseudocounts

80


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

38


BA10H 
Estimate the Parameters of an HMM

57


BA10I 
Implement Viterbi Learning

46


BA10J 
Solve the Soft Decoding Problem

47


BA10K 
Implement BaumWelch Learning

34


BA11A 
Construct the Graph of a Spectrum

80


BA11B 
Implement DecodingIdealSpectrum

56


BA11C 
Convert a Peptide into a Peptide Vector

84


BA11D 
Convert a Peptide Vector into a Peptide

78


BA11E 
Sequence a Peptide

45


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

47


BA11G 
Implement PSMSearch

45


BA11H 
Compute the Size of a Spectral Dictionary

38


BA11I 
Compute the Probability of a Spectral Dictionary

37


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

29


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

649


BA1B 
Find the Most Frequent Words in a String

807


BA1C 
Find the Reverse Complement of a String

775


BA1D 
Find All Occurrences of a Pattern in a String

691


BA1E 
Find Patterns Forming Clumps in a String

531


BA1F 
Find a Position in a Genome Minimizing the Skew

525


BA1G 
Compute the Hamming Distance Between Two Strings

532


BA1H 
Find All Approximate Occurrences of a Pattern in a String

514


BA1I 
Find the Most Frequent Words with Mismatches in a String

410


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

365


BA1K 
Generate the Frequency Array of a String

327


BA1L 
Implement PatternToNumber

368


BA1M 
Implement NumberToPattern

334


BA1N 
Generate the dNeighborhood of a String

372


BA2A 
Implement MotifEnumeration

320


BA2B 
Find a Median String

292


BA2C 
Find a Profilemost Probable kmer in a String

320


BA2D 
Implement GreedyMotifSearch

261


BA2E 
Implement GreedyMotifSearch with Pseudocounts

215


BA2F 
Implement RandomizedMotifSearch

171


BA2G 
Implement GibbsSampler

153


BA2H 
Implement DistanceBetweenPatternAndStrings

203


BA3A 
Generate the kmer Composition of a String

341


BA3B 
Reconstruct a String from its Genome Path

278


BA3C 
Construct the Overlap Graph of a Collection of kmers

287


BA3D 
Construct the De Bruijn Graph of a String

271


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

253


BA3F 
Find an Eulerian Cycle in a Graph

188


BA3G 
Find an Eulerian Path in a Graph

171


BA3H 
Reconstruct a String from its kmer Composition

166


BA3I 
Find a kUniversal Circular String

133


BA3J 
Reconstruct a String from its Paired Composition

105


BA3K 
Generate Contigs from a Collection of Reads

117


BA3L 
Construct a String Spelled by a Gapped Genome Path

98


BA3M 
Generate All Maximal NonBranching Paths in a Graph

95


BA4A 
Translate an RNA String into an Amino Acid String

235


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

183


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

182


BA4D 
Compute the Number of Peptides of Given Total Mass

101


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

129


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

106


BA4G 
Implement LeaderboardCyclopeptideSequencing

104


BA4H 
Generate the Convolution of a Spectrum

104


BA4I 
Implement ConvolutionCyclopeptideSequencing

73


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

109


BA4K 
Compute the Score of a Linear Peptide

92


BA4L 
Trim a Peptide Leaderboard

80


BA4M 
Solve the Turnpike Problem

50


BA5A 
Find the Minimum Number of Coins Needed to Make Change

400


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

328


BA5C 
Find a Longest Common Subsequence of Two Strings

387


BA5D 
Find the Longest Path in a DAG

265


BA5E 
Find a HighestScoring Alignment of Two Strings

313


BA5F 
Find a HighestScoring Local Alignment of Two Strings

272


BA5G 
Compute the Edit Distance Between Two Strings

327


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

226


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

208


BA5J 
Align Two Strings Using Affine Gap Penalties

194


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

126


BA5L 
Align Two Strings Using Linear Space

108


BA5M 
Find a HighestScoring Multiple Sequence Alignment

131


BA5N 
Find a Topological Ordering of a DAG

82


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

237


BA6B 
Compute the Number of Breakpoints in a Permutation

257


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

165


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

39


BA6E 
Find All Shared kmers of a Pair of Strings

174


BA6F 
Implement ChromosomeToCycle

94


BA6G 
Implement CycleToChromosome

89


BA6H 
Implement ColoredEdges

81


BA6I 
Implement GraphToGenome

65


BA6J 
Implement 2BreakOnGenomeGraph

59


BA6K 
Implement 2BreakOnGenome

44


BA7A 
Compute Distances Between Leaves

105


BA7B 
Compute Limb Lengths in a Tree

95


BA7C 
Implement AdditivePhylogeny

64


BA7D 
Implement UPGMA

60


BA7E 
Implement the Neighbor Joining Algorithm

53


BA7F 
Implement SmallParsimony

47


BA7G 
Adapt SmallParsimony to Unrooted Trees

29


BA8A 
Implement FarthestFirstTraversal

80


BA8B 
Compute the Squared Error Distortion

76


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

69


BA8D 
Implement the Soft kMeans Clustering Algorithm

64


BA8E 
Implement Hierarchical Clustering

63


BA9A 
Construct a Trie from a Collection of Patterns

200


BA9B 
Implement TrieMatching

178


BA9C 
Construct the Suffix Tree of a String

139


BA9D 
Find the Longest Repeat in a String

164


BA9E 
Find the Longest Substring Shared by Two Strings

154


BA9F 
Find the Shortest NonShared Substring of Two Strings

123


BA9G 
Construct the Suffix Array of a String

160


BA9H 
Pattern Matching with the Suffix Array

79


BA9I 
Construct the BurrowsWheeler Transform of a String

187


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

154


BA9K 
Generate the LasttoFirst Mapping of a String

83


BA9L 
Implement BWMatching

117


BA9M 
Implement BetterBWMatching

110


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

122


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

93


BA9P 
Implement TreeColoring

41


BA9Q 
Construct the Partial Suffix Array of a String

97


BA9R 
Construct a Suffix Tree from a Suffix Array

70

