BA10A 
Compute the Probability of a Hidden Path

291


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

244


BA10C 
Implement the Viterbi Algorithm

151


BA10D 
Compute the Probability of a String Emitted by an HMM

136


BA10E 
Construct a Profile HMM

89


BA10F 
Construct a Profile HMM with Pseudocounts

79


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

37


BA10H 
Estimate the Parameters of an HMM

55


BA10I 
Implement Viterbi Learning

44


BA10J 
Solve the Soft Decoding Problem

45


BA10K 
Implement BaumWelch Learning

32


BA11A 
Construct the Graph of a Spectrum

78


BA11B 
Implement DecodingIdealSpectrum

56


BA11C 
Convert a Peptide into a Peptide Vector

83


BA11D 
Convert a Peptide Vector into a Peptide

77


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

627


BA1B 
Find the Most Frequent Words in a String

789


BA1C 
Find the Reverse Complement of a String

718


BA1D 
Find All Occurrences of a Pattern in a String

679


BA1E 
Find Patterns Forming Clumps in a String

526


BA1F 
Find a Position in a Genome Minimizing the Skew

519


BA1G 
Compute the Hamming Distance Between Two Strings

525


BA1H 
Find All Approximate Occurrences of a Pattern in a String

510


BA1I 
Find the Most Frequent Words with Mismatches in a String

404


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

363


BA1K 
Generate the Frequency Array of a String

323


BA1L 
Implement PatternToNumber

363


BA1M 
Implement NumberToPattern

330


BA1N 
Generate the dNeighborhood of a String

352


BA2A 
Implement MotifEnumeration

312


BA2B 
Find a Median String

278


BA2C 
Find a Profilemost Probable kmer in a String

299


BA2D 
Implement GreedyMotifSearch

234


BA2E 
Implement GreedyMotifSearch with Pseudocounts

198


BA2F 
Implement RandomizedMotifSearch

161


BA2G 
Implement GibbsSampler

148


BA2H 
Implement DistanceBetweenPatternAndStrings

196


BA3A 
Generate the kmer Composition of a String

327


BA3B 
Reconstruct a String from its Genome Path

265


BA3C 
Construct the Overlap Graph of a Collection of kmers

274


BA3D 
Construct the De Bruijn Graph of a String

265


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

249


BA3F 
Find an Eulerian Cycle in a Graph

185


BA3G 
Find an Eulerian Path in a Graph

167


BA3H 
Reconstruct a String from its kmer Composition

163


BA3I 
Find a kUniversal Circular String

131


BA3J 
Reconstruct a String from its Paired Composition

103


BA3K 
Generate Contigs from a Collection of Reads

115


BA3L 
Construct a String Spelled by a Gapped Genome Path

96


BA3M 
Generate All Maximal NonBranching Paths in a Graph

93


BA4A 
Translate an RNA String into an Amino Acid String

232


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

177


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

179


BA4D 
Compute the Number of Peptides of Given Total Mass

98


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

125


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

103


BA4G 
Implement LeaderboardCyclopeptideSequencing

102


BA4H 
Generate the Convolution of a Spectrum

102


BA4I 
Implement ConvolutionCyclopeptideSequencing

71


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

106


BA4K 
Compute the Score of a Linear Peptide

89


BA4L 
Trim a Peptide Leaderboard

78


BA4M 
Solve the Turnpike Problem

50


BA5A 
Find the Minimum Number of Coins Needed to Make Change

398


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

328


BA5C 
Find a Longest Common Subsequence of Two Strings

386


BA5D 
Find the Longest Path in a DAG

265


BA5E 
Find a HighestScoring Alignment of Two Strings

309


BA5F 
Find a HighestScoring Local Alignment of Two Strings

271


BA5G 
Compute the Edit Distance Between Two Strings

324


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

224


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

206


BA5J 
Align Two Strings Using Affine Gap Penalties

193


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

236


BA6B 
Compute the Number of Breakpoints in a Permutation

255


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

104


BA7B 
Compute Limb Lengths in a Tree

95


BA7C 
Implement AdditivePhylogeny

63


BA7D 
Implement UPGMA

59


BA7E 
Implement the Neighbor Joining Algorithm

52


BA7F 
Implement SmallParsimony

45


BA7G 
Adapt SmallParsimony to Unrooted Trees

28


BA8A 
Implement FarthestFirstTraversal

79


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

198


BA9B 
Implement TrieMatching

177


BA9C 
Construct the Suffix Tree of a String

139


BA9D 
Find the Longest Repeat in a String

163


BA9E 
Find the Longest Substring Shared by Two Strings

153


BA9F 
Find the Shortest NonShared Substring of Two Strings

122


BA9G 
Construct the Suffix Array of a String

159


BA9H 
Pattern Matching with the Suffix Array

79


BA9I 
Construct the BurrowsWheeler Transform of a String

183


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

152


BA9K 
Generate the LasttoFirst Mapping of a String

82


BA9L 
Implement BWMatching

116


BA9M 
Implement BetterBWMatching

108


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

92


BA9P 
Implement TreeColoring

41


BA9Q 
Construct the Partial Suffix Array of a String

96


BA9R 
Construct a Suffix Tree from a Suffix Array

70

