BA10A 
Compute the Probability of a Hidden Path

269


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

225


BA10C 
Implement the Viterbi Algorithm

142


BA10D 
Compute the Probability of a String Emitted by an HMM

128


BA10E 
Construct a Profile HMM

85


BA10F 
Construct a Profile HMM with Pseudocounts

75


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

34


BA10H 
Estimate the Parameters of an HMM

51


BA10I 
Implement Viterbi Learning

40


BA10J 
Solve the Soft Decoding Problem

44


BA10K 
Implement BaumWelch Learning

31


BA11A 
Construct the Graph of a Spectrum

70


BA11B 
Implement DecodingIdealSpectrum

50


BA11C 
Convert a Peptide into a Peptide Vector

74


BA11D 
Convert a Peptide Vector into a Peptide

68


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

36


BA11I 
Compute the Probability of a Spectral Dictionary

35


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

26


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

527


BA1B 
Find the Most Frequent Words in a String

710


BA1C 
Find the Reverse Complement of a String

640


BA1D 
Find All Occurrences of a Pattern in a String

602


BA1E 
Find Patterns Forming Clumps in a String

480


BA1F 
Find a Position in a Genome Minimizing the Skew

463


BA1G 
Compute the Hamming Distance Between Two Strings

451


BA1H 
Find All Approximate Occurrences of a Pattern in a String

464


BA1I 
Find the Most Frequent Words with Mismatches in a String

366


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

331


BA1K 
Generate the Frequency Array of a String

292


BA1L 
Implement PatternToNumber

329


BA1M 
Implement NumberToPattern

298


BA1N 
Generate the dNeighborhood of a String

323


BA2A 
Implement MotifEnumeration

278


BA2B 
Find a Median String

240


BA2C 
Find a Profilemost Probable kmer in a String

260


BA2D 
Implement GreedyMotifSearch

212


BA2E 
Implement GreedyMotifSearch with Pseudocounts

180


BA2F 
Implement RandomizedMotifSearch

148


BA2G 
Implement GibbsSampler

137


BA2H 
Implement DistanceBetweenPatternAndStrings

169


BA3A 
Generate the kmer Composition of a String

297


BA3B 
Reconstruct a String from its Genome Path

240


BA3C 
Construct the Overlap Graph of a Collection of kmers

254


BA3D 
Construct the De Bruijn Graph of a String

243


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

225


BA3F 
Find an Eulerian Cycle in a Graph

170


BA3G 
Find an Eulerian Path in a Graph

156


BA3H 
Reconstruct a String from its kmer Composition

152


BA3I 
Find a kUniversal Circular String

121


BA3J 
Reconstruct a String from its Paired Composition

94


BA3K 
Generate Contigs from a Collection of Reads

106


BA3L 
Construct a String Spelled by a Gapped Genome Path

87


BA3M 
Generate All Maximal NonBranching Paths in a Graph

87


BA4A 
Translate an RNA String into an Amino Acid String

211


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

167


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

170


BA4D 
Compute the Number of Peptides of Given Total Mass

86


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

113


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

96


BA4G 
Implement LeaderboardCyclopeptideSequencing

95


BA4H 
Generate the Convolution of a Spectrum

97


BA4I 
Implement ConvolutionCyclopeptideSequencing

67


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

100


BA4K 
Compute the Score of a Linear Peptide

83


BA4L 
Trim a Peptide Leaderboard

73


BA4M 
Solve the Turnpike Problem

45


BA5A 
Find the Minimum Number of Coins Needed to Make Change

370


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

311


BA5C 
Find a Longest Common Subsequence of Two Strings

375


BA5D 
Find the Longest Path in a DAG

255


BA5E 
Find a HighestScoring Alignment of Two Strings

293


BA5F 
Find a HighestScoring Local Alignment of Two Strings

255


BA5G 
Compute the Edit Distance Between Two Strings

314


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

216


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

198


BA5J 
Align Two Strings Using Affine Gap Penalties

186


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

122


BA5L 
Align Two Strings Using Linear Space

104


BA5M 
Find a HighestScoring Multiple Sequence Alignment

127


BA5N 
Find a Topological Ordering of a DAG

77


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

169


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

98


BA7B 
Compute Limb Lengths in a Tree

89


BA7C 
Implement AdditivePhylogeny

60


BA7D 
Implement UPGMA

55


BA7E 
Implement the Neighbor Joining Algorithm

49


BA7F 
Implement SmallParsimony

42


BA7G 
Adapt SmallParsimony to Unrooted Trees

26


BA8A 
Implement FarthestFirstTraversal

72


BA8B 
Compute the Squared Error Distortion

70


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

64


BA8D 
Implement the Soft kMeans Clustering Algorithm

60


BA8E 
Implement Hierarchical Clustering

51


BA9A 
Construct a Trie from a Collection of Patterns

192


BA9B 
Implement TrieMatching

169


BA9C 
Construct the Suffix Tree of a String

131


BA9D 
Find the Longest Repeat in a String

148


BA9E 
Find the Longest Substring Shared by Two Strings

146


BA9F 
Find the Shortest NonShared Substring of Two Strings

114


BA9G 
Construct the Suffix Array of a String

149


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

64


BA9L 
Implement BWMatching

110


BA9M 
Implement BetterBWMatching

104


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

116


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

67

