BA10A 
Compute the Probability of a Hidden Path

275


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

233


BA10C 
Implement the Viterbi Algorithm

148


BA10D 
Compute the Probability of a String Emitted by an HMM

133


BA10E 
Construct a Profile HMM

86


BA10F 
Construct a Profile HMM with Pseudocounts

76


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

35


BA10H 
Estimate the Parameters of an HMM

53


BA10I 
Implement Viterbi Learning

42


BA10J 
Solve the Soft Decoding Problem

44


BA10K 
Implement BaumWelch Learning

31


BA11A 
Construct the Graph of a Spectrum

72


BA11B 
Implement DecodingIdealSpectrum

52


BA11C 
Convert a Peptide into a Peptide Vector

77


BA11D 
Convert a Peptide Vector into a Peptide

71


BA11E 
Sequence a Peptide

43


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

45


BA11G 
Implement PSMSearch

43


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

541


BA1B 
Find the Most Frequent Words in a String

725


BA1C 
Find the Reverse Complement of a String

652


BA1D 
Find All Occurrences of a Pattern in a String

614


BA1E 
Find Patterns Forming Clumps in a String

490


BA1F 
Find a Position in a Genome Minimizing the Skew

472


BA1G 
Compute the Hamming Distance Between Two Strings

461


BA1H 
Find All Approximate Occurrences of a Pattern in a String

471


BA1I 
Find the Most Frequent Words with Mismatches in a String

376


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

337


BA1K 
Generate the Frequency Array of a String

298


BA1L 
Implement PatternToNumber

335


BA1M 
Implement NumberToPattern

304


BA1N 
Generate the dNeighborhood of a String

329


BA2A 
Implement MotifEnumeration

282


BA2B 
Find a Median String

244


BA2C 
Find a Profilemost Probable kmer in a String

264


BA2D 
Implement GreedyMotifSearch

215


BA2E 
Implement GreedyMotifSearch with Pseudocounts

183


BA2F 
Implement RandomizedMotifSearch

150


BA2G 
Implement GibbsSampler

139


BA2H 
Implement DistanceBetweenPatternAndStrings

173


BA3A 
Generate the kmer Composition of a String

300


BA3B 
Reconstruct a String from its Genome Path

242


BA3C 
Construct the Overlap Graph of a Collection of kmers

261


BA3D 
Construct the De Bruijn Graph of a String

249


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

232


BA3F 
Find an Eulerian Cycle in a Graph

176


BA3G 
Find an Eulerian Path in a Graph

162


BA3H 
Reconstruct a String from its kmer Composition

153


BA3I 
Find a kUniversal Circular String

122


BA3J 
Reconstruct a String from its Paired Composition

96


BA3K 
Generate Contigs from a Collection of Reads

107


BA3L 
Construct a String Spelled by a Gapped Genome Path

88


BA3M 
Generate All Maximal NonBranching Paths in a Graph

88


BA4A 
Translate an RNA String into an Amino Acid String

214


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

87


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

117


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

97


BA4G 
Implement LeaderboardCyclopeptideSequencing

97


BA4H 
Generate the Convolution of a Spectrum

98


BA4I 
Implement ConvolutionCyclopeptideSequencing

68


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

100


BA4K 
Compute the Score of a Linear Peptide

84


BA4L 
Trim a Peptide Leaderboard

74


BA4M 
Solve the Turnpike Problem

46


BA5A 
Find the Minimum Number of Coins Needed to Make Change

376


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

313


BA5C 
Find a Longest Common Subsequence of Two Strings

378


BA5D 
Find the Longest Path in a DAG

259


BA5E 
Find a HighestScoring Alignment of Two Strings

300


BA5F 
Find a HighestScoring Local Alignment of Two Strings

263


BA5G 
Compute the Edit Distance Between Two Strings

318


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

221


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

204


BA5J 
Align Two Strings Using Affine Gap Penalties

190


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

124


BA5L 
Align Two Strings Using Linear Space

106


BA5M 
Find a HighestScoring Multiple Sequence Alignment

128


BA5N 
Find a Topological Ordering of a DAG

78


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

229


BA6B 
Compute the Number of Breakpoints in a Permutation

246


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

160


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

34


BA6E 
Find All Shared kmers of a Pair of Strings

170


BA6F 
Implement ChromosomeToCycle

89


BA6G 
Implement CycleToChromosome

84


BA6H 
Implement ColoredEdges

78


BA6I 
Implement GraphToGenome

62


BA6J 
Implement 2BreakOnGenomeGraph

58


BA6K 
Implement 2BreakOnGenome

41


BA7A 
Compute Distances Between Leaves

99


BA7B 
Compute Limb Lengths in a Tree

90


BA7C 
Implement AdditivePhylogeny

61


BA7D 
Implement UPGMA

56


BA7E 
Implement the Neighbor Joining Algorithm

50


BA7F 
Implement SmallParsimony

42


BA7G 
Adapt SmallParsimony to Unrooted Trees

26


BA8A 
Implement FarthestFirstTraversal

75


BA8B 
Compute the Squared Error Distortion

73


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

65


BA8D 
Implement the Soft kMeans Clustering Algorithm

61


BA8E 
Implement Hierarchical Clustering

58


BA9A 
Construct a Trie from a Collection of Patterns

194


BA9B 
Implement TrieMatching

172


BA9C 
Construct the Suffix Tree of a String

133


BA9D 
Find the Longest Repeat in a String

158


BA9E 
Find the Longest Substring Shared by Two Strings

151


BA9F 
Find the Shortest NonShared Substring of Two Strings

119


BA9G 
Construct the Suffix Array of a String

151


BA9H 
Pattern Matching with the Suffix Array

73


BA9I 
Construct the BurrowsWheeler Transform of a String

175


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

145


BA9K 
Generate the LasttoFirst Mapping of a String

76


BA9L 
Implement BWMatching

112


BA9M 
Implement BetterBWMatching

106


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

118


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

89


BA9P 
Implement TreeColoring

38


BA9Q 
Construct the Partial Suffix Array of a String

94


BA9R 
Construct a Suffix Tree from a Suffix Array

67

