BA10A 
Compute the Probability of a Hidden Path

464


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

389


BA10C 
Implement the Viterbi Algorithm

245


BA10D 
Compute the Probability of a String Emitted by an HMM

209


BA10E 
Construct a Profile HMM

132


BA10F 
Construct a Profile HMM with Pseudocounts

121


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

66


BA10H 
Estimate the Parameters of an HMM

87


BA10I 
Implement Viterbi Learning

77


BA10J 
Solve the Soft Decoding Problem

80


BA10K 
Implement BaumWelch Learning

63


BA11A 
Construct the Graph of a Spectrum

113


BA11B 
Implement DecodingIdealSpectrum

86


BA11C 
Convert a Peptide into a Peptide Vector

118


BA11D 
Convert a Peptide Vector into a Peptide

113


BA11E 
Sequence a Peptide

68


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

68


BA11G 
Implement PSMSearch

67


BA11H 
Compute the Size of a Spectral Dictionary

56


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

1037


BA1B 
Find the Most Frequent Words in a String

1221


BA1C 
Find the Reverse Complement of a String

1170


BA1D 
Find All Occurrences of a Pattern in a String

1080


BA1E 
Find Patterns Forming Clumps in a String

836


BA1F 
Find a Position in a Genome Minimizing the Skew

831


BA1G 
Compute the Hamming Distance Between Two Strings

881


BA1H 
Find All Approximate Occurrences of a Pattern in a String

765


BA1I 
Find the Most Frequent Words with Mismatches in a String

626


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

563


BA1K 
Generate the Frequency Array of a String

508


BA1L 
Implement PatternToNumber

570


BA1M 
Implement NumberToPattern

528


BA1N 
Generate the dNeighborhood of a String

554


BA2A 
Implement MotifEnumeration

457


BA2B 
Find a Median String

458


BA2C 
Find a Profilemost Probable kmer in a String

479


BA2D 
Implement GreedyMotifSearch

394


BA2E 
Implement GreedyMotifSearch with Pseudocounts

339


BA2F 
Implement RandomizedMotifSearch

274


BA2G 
Implement GibbsSampler

246


BA2H 
Implement DistanceBetweenPatternAndStrings

314


BA3A 
Generate the kmer Composition of a String

582


BA3B 
Reconstruct a String from its Genome Path

513


BA3C 
Construct the Overlap Graph of a Collection of kmers

484


BA3D 
Construct the De Bruijn Graph of a String

484


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

441


BA3F 
Find an Eulerian Cycle in a Graph

333


BA3G 
Find an Eulerian Path in a Graph

276


BA3H 
Reconstruct a String from its kmer Composition

278


BA3I 
Find a kUniversal Circular String

220


BA3J 
Reconstruct a String from its Paired Composition

196


BA3K 
Generate Contigs from a Collection of Reads

196


BA3L 
Construct a String Spelled by a Gapped Genome Path

162


BA3M 
Generate All Maximal NonBranching Paths in a Graph

143


BA4A 
Translate an RNA String into an Amino Acid String

377


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

290


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

280


BA4D 
Compute the Number of Peptides of Given Total Mass

175


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

213


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

172


BA4G 
Implement LeaderboardCyclopeptideSequencing

163


BA4H 
Generate the Convolution of a Spectrum

166


BA4I 
Implement ConvolutionCyclopeptideSequencing

122


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

187


BA4K 
Compute the Score of a Linear Peptide

146


BA4L 
Trim a Peptide Leaderboard

130


BA4M 
Solve the Turnpike Problem

77


BA5A 
Find the Minimum Number of Coins Needed to Make Change

494


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

404


BA5C 
Find a Longest Common Subsequence of Two Strings

497


BA5D 
Find the Longest Path in a DAG

330


BA5E 
Find a HighestScoring Alignment of Two Strings

464


BA5F 
Find a HighestScoring Local Alignment of Two Strings

378


BA5G 
Compute the Edit Distance Between Two Strings

449


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

275


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

252


BA5J 
Align Two Strings Using Affine Gap Penalties

283


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

182


BA5L 
Align Two Strings Using Linear Space

162


BA5M 
Find a HighestScoring Multiple Sequence Alignment

182


BA5N 
Find a Topological Ordering of a DAG

127


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

287


BA6B 
Compute the Number of Breakpoints in a Permutation

315


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

208


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

66


BA6E 
Find All Shared kmers of a Pair of Strings

211


BA6F 
Implement ChromosomeToCycle

126


BA6G 
Implement CycleToChromosome

122


BA6H 
Implement ColoredEdges

112


BA6I 
Implement GraphToGenome

92


BA6J 
Implement 2BreakOnGenomeGraph

86


BA6K 
Implement 2BreakOnGenome

78


BA7A 
Compute Distances Between Leaves

143


BA7B 
Compute Limb Lengths in a Tree

153


BA7C 
Implement AdditivePhylogeny

108


BA7D 
Implement UPGMA

106


BA7E 
Implement the Neighbor Joining Algorithm

89


BA7F 
Implement SmallParsimony

80


BA7G 
Adapt SmallParsimony to Unrooted Trees

49


BA8A 
Implement FarthestFirstTraversal

115


BA8B 
Compute the Squared Error Distortion

108


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

120


BA8D 
Implement the Soft kMeans Clustering Algorithm

96


BA8E 
Implement Hierarchical Clustering

92


BA9A 
Construct a Trie from a Collection of Patterns

244


BA9B 
Implement TrieMatching

218


BA9C 
Construct the Suffix Tree of a String

170


BA9D 
Find the Longest Repeat in a String

201


BA9E 
Find the Longest Substring Shared by Two Strings

185


BA9F 
Find the Shortest NonShared Substring of Two Strings

150


BA9G 
Construct the Suffix Array of a String

204


BA9H 
Pattern Matching with the Suffix Array

112


BA9I 
Construct the BurrowsWheeler Transform of a String

242


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

199


BA9K 
Generate the LasttoFirst Mapping of a String

129


BA9L 
Implement BWMatching

157


BA9M 
Implement BetterBWMatching

141


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

153


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

120


BA9P 
Implement TreeColoring

62


BA9Q 
Construct the Partial Suffix Array of a String

121


BA9R 
Construct a Suffix Tree from a Suffix Array

92

