BA10A 
Compute the Probability of a Hidden Path

493


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

418


BA10C 
Implement the Viterbi Algorithm

256


BA10D 
Compute the Probability of a String Emitted by an HMM

218


BA10E 
Construct a Profile HMM

134


BA10F 
Construct a Profile HMM with Pseudocounts

123


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

68


BA10H 
Estimate the Parameters of an HMM

92


BA10I 
Implement Viterbi Learning

79


BA10J 
Solve the Soft Decoding Problem

85


BA10K 
Implement BaumWelch Learning

67


BA11A 
Construct the Graph of a Spectrum

114


BA11B 
Implement DecodingIdealSpectrum

87


BA11C 
Convert a Peptide into a Peptide Vector

119


BA11D 
Convert a Peptide Vector into a Peptide

114


BA11E 
Sequence a Peptide

70


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

69


BA11G 
Implement PSMSearch

67


BA11H 
Compute the Size of a Spectral Dictionary

57


BA11I 
Compute the Probability of a Spectral Dictionary

56


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

45


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

1157


BA1B 
Find the Most Frequent Words in a String

1331


BA1C 
Find the Reverse Complement of a String

1289


BA1D 
Find All Occurrences of a Pattern in a String

1194


BA1E 
Find Patterns Forming Clumps in a String

930


BA1F 
Find a Position in a Genome Minimizing the Skew

945


BA1G 
Compute the Hamming Distance Between Two Strings

980


BA1H 
Find All Approximate Occurrences of a Pattern in a String

865


BA1I 
Find the Most Frequent Words with Mismatches in a String

713


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

651


BA1K 
Generate the Frequency Array of a String

599


BA1L 
Implement PatternToNumber

649


BA1M 
Implement NumberToPattern

617


BA1N 
Generate the dNeighborhood of a String

627


BA2A 
Implement MotifEnumeration

520


BA2B 
Find a Median String

536


BA2C 
Find a Profilemost Probable kmer in a String

544


BA2D 
Implement GreedyMotifSearch

459


BA2E 
Implement GreedyMotifSearch with Pseudocounts

400


BA2F 
Implement RandomizedMotifSearch

320


BA2G 
Implement GibbsSampler

273


BA2H 
Implement DistanceBetweenPatternAndStrings

366


BA3A 
Generate the kmer Composition of a String

652


BA3B 
Reconstruct a String from its Genome Path

584


BA3C 
Construct the Overlap Graph of a Collection of kmers

533


BA3D 
Construct the De Bruijn Graph of a String

545


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

486


BA3F 
Find an Eulerian Cycle in a Graph

378


BA3G 
Find an Eulerian Path in a Graph

320


BA3H 
Reconstruct a String from its kmer Composition

333


BA3I 
Find a kUniversal Circular String

252


BA3J 
Reconstruct a String from its Paired Composition

218


BA3K 
Generate Contigs from a Collection of Reads

212


BA3L 
Construct a String Spelled by a Gapped Genome Path

183


BA3M 
Generate All Maximal NonBranching Paths in a Graph

159


BA4A 
Translate an RNA String into an Amino Acid String

433


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

350


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

332


BA4D 
Compute the Number of Peptides of Given Total Mass

220


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

251


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

203


BA4G 
Implement LeaderboardCyclopeptideSequencing

187


BA4H 
Generate the Convolution of a Spectrum

191


BA4I 
Implement ConvolutionCyclopeptideSequencing

136


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

209


BA4K 
Compute the Score of a Linear Peptide

164


BA4L 
Trim a Peptide Leaderboard

148


BA4M 
Solve the Turnpike Problem

80


BA5A 
Find the Minimum Number of Coins Needed to Make Change

532


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

425


BA5C 
Find a Longest Common Subsequence of Two Strings

517


BA5D 
Find the Longest Path in a DAG

341


BA5E 
Find a HighestScoring Alignment of Two Strings

496


BA5F 
Find a HighestScoring Local Alignment of Two Strings

409


BA5G 
Compute the Edit Distance Between Two Strings

463


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

293


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

262


BA5J 
Align Two Strings Using Affine Gap Penalties

290


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

188


BA5L 
Align Two Strings Using Linear Space

167


BA5M 
Find a HighestScoring Multiple Sequence Alignment

185


BA5N 
Find a Topological Ordering of a DAG

133


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

302


BA6B 
Compute the Number of Breakpoints in a Permutation

331


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

220


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

71


BA6E 
Find All Shared kmers of a Pair of Strings

213


BA6F 
Implement ChromosomeToCycle

130


BA6G 
Implement CycleToChromosome

126


BA6H 
Implement ColoredEdges

116


BA6I 
Implement GraphToGenome

95


BA6J 
Implement 2BreakOnGenomeGraph

89


BA6K 
Implement 2BreakOnGenome

86


BA7A 
Compute Distances Between Leaves

155


BA7B 
Compute Limb Lengths in a Tree

163


BA7C 
Implement AdditivePhylogeny

120


BA7D 
Implement UPGMA

122


BA7E 
Implement the Neighbor Joining Algorithm

99


BA7F 
Implement SmallParsimony

86


BA7G 
Adapt SmallParsimony to Unrooted Trees

56


BA8A 
Implement FarthestFirstTraversal

117


BA8B 
Compute the Squared Error Distortion

110


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

123


BA8D 
Implement the Soft kMeans Clustering Algorithm

98


BA8E 
Implement Hierarchical Clustering

95


BA9A 
Construct a Trie from a Collection of Patterns

260


BA9B 
Implement TrieMatching

234


BA9C 
Construct the Suffix Tree of a String

176


BA9D 
Find the Longest Repeat in a String

204


BA9E 
Find the Longest Substring Shared by Two Strings

187


BA9F 
Find the Shortest NonShared Substring of Two Strings

153


BA9G 
Construct the Suffix Array of a String

218


BA9H 
Pattern Matching with the Suffix Array

120


BA9I 
Construct the BurrowsWheeler Transform of a String

265


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

212


BA9K 
Generate the LasttoFirst Mapping of a String

141


BA9L 
Implement BWMatching

165


BA9M 
Implement BetterBWMatching

150


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

157


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

129


BA9P 
Implement TreeColoring

64


BA9Q 
Construct the Partial Suffix Array of a String

125


BA9R 
Construct a Suffix Tree from a Suffix Array

93

