BA10A 
Compute the Probability of a Hidden Path

619


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

516


BA10C 
Implement the Viterbi Algorithm

311


BA10D 
Compute the Probability of a String Emitted by an HMM

254


BA10E 
Construct a Profile HMM

155


BA10F 
Construct a Profile HMM with Pseudocounts

145


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

81


BA10H 
Estimate the Parameters of an HMM

120


BA10I 
Implement Viterbi Learning

97


BA10J 
Solve the Soft Decoding Problem

102


BA10K 
Implement BaumWelch Learning

80


BA11A 
Construct the Graph of a Spectrum

139


BA11B 
Implement DecodingIdealSpectrum

99


BA11C 
Convert a Peptide into a Peptide Vector

146


BA11D 
Convert a Peptide Vector into a Peptide

141


BA11E 
Sequence a Peptide

81


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

81


BA11G 
Implement PSMSearch

78


BA11H 
Compute the Size of a Spectral Dictionary

69


BA11I 
Compute the Probability of a Spectral Dictionary

68


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

54


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

1589


BA1B 
Find the Most Frequent Words in a String

1747


BA1C 
Find the Reverse Complement of a String

1675


BA1D 
Find All Occurrences of a Pattern in a String

1558


BA1E 
Find Patterns Forming Clumps in a String

1263


BA1F 
Find a Position in a Genome Minimizing the Skew

1273


BA1G 
Compute the Hamming Distance Between Two Strings

1324


BA1H 
Find All Approximate Occurrences of a Pattern in a String

1131


BA1I 
Find the Most Frequent Words with Mismatches in a String

923


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

839


BA1K 
Generate the Frequency Array of a String

747


BA1L 
Implement PatternToNumber

823


BA1M 
Implement NumberToPattern

781


BA1N 
Generate the dNeighborhood of a String

775


BA2A 
Implement MotifEnumeration

668


BA2B 
Find a Median String

695


BA2C 
Find a Profilemost Probable kmer in a String

695


BA2D 
Implement GreedyMotifSearch

605


BA2E 
Implement GreedyMotifSearch with Pseudocounts

535


BA2F 
Implement RandomizedMotifSearch

438


BA2G 
Implement GibbsSampler

377


BA2H 
Implement DistanceBetweenPatternAndStrings

479


BA3A 
Generate the kmer Composition of a String

849


BA3B 
Reconstruct a String from its Genome Path

768


BA3C 
Construct the Overlap Graph of a Collection of kmers

716


BA3D 
Construct the De Bruijn Graph of a String

740


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

650


BA3F 
Find an Eulerian Cycle in a Graph

492


BA3G 
Find an Eulerian Path in a Graph

440


BA3H 
Reconstruct a String from its kmer Composition

506


BA3I 
Find a kUniversal Circular String

348


BA3J 
Reconstruct a String from its Paired Composition

302


BA3K 
Generate Contigs from a Collection of Reads

286


BA3L 
Construct a String Spelled by a Gapped Genome Path

259


BA3M 
Generate All Maximal NonBranching Paths in a Graph

218


BA4A 
Translate an RNA String into an Amino Acid String

559


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

470


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

437


BA4D 
Compute the Number of Peptides of Given Total Mass

308


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

349


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

269


BA4G 
Implement LeaderboardCyclopeptideSequencing

258


BA4H 
Generate the Convolution of a Spectrum

254


BA4I 
Implement ConvolutionCyclopeptideSequencing

180


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

270


BA4K 
Compute the Score of a Linear Peptide

217


BA4L 
Trim a Peptide Leaderboard

195


BA4M 
Solve the Turnpike Problem

115


BA5A 
Find the Minimum Number of Coins Needed to Make Change

637


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

509


BA5C 
Find a Longest Common Subsequence of Two Strings

643


BA5D 
Find the Longest Path in a DAG

400


BA5E 
Find a HighestScoring Alignment of Two Strings

596


BA5F 
Find a HighestScoring Local Alignment of Two Strings

470


BA5G 
Compute the Edit Distance Between Two Strings

525


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

339


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

304


BA5J 
Align Two Strings Using Affine Gap Penalties

344


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

218


BA5L 
Align Two Strings Using Linear Space

190


BA5M 
Find a HighestScoring Multiple Sequence Alignment

226


BA5N 
Find a Topological Ordering of a DAG

168


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

350


BA6B 
Compute the Number of Breakpoints in a Permutation

387


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

255


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

92


BA6E 
Find All Shared kmers of a Pair of Strings

227


BA6F 
Implement ChromosomeToCycle

156


BA6G 
Implement CycleToChromosome

150


BA6H 
Implement ColoredEdges

141


BA6I 
Implement GraphToGenome

114


BA6J 
Implement 2BreakOnGenomeGraph

119


BA6K 
Implement 2BreakOnGenome

104


BA7A 
Compute Distances Between Leaves

204


BA7B 
Compute Limb Lengths in a Tree

224


BA7C 
Implement AdditivePhylogeny

173


BA7D 
Implement UPGMA

154


BA7E 
Implement the Neighbor Joining Algorithm

155


BA7F 
Implement SmallParsimony

111


BA7G 
Adapt SmallParsimony to Unrooted Trees

76


BA8A 
Implement FarthestFirstTraversal

146


BA8B 
Compute the Squared Error Distortion

140


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

154


BA8D 
Implement the Soft kMeans Clustering Algorithm

110


BA8E 
Implement Hierarchical Clustering

117


BA9A 
Construct a Trie from a Collection of Patterns

292


BA9B 
Implement TrieMatching

270


BA9C 
Construct the Suffix Tree of a String

203


BA9D 
Find the Longest Repeat in a String

232


BA9E 
Find the Longest Substring Shared by Two Strings

210


BA9F 
Find the Shortest NonShared Substring of Two Strings

174


BA9G 
Construct the Suffix Array of a String

258


BA9H 
Pattern Matching with the Suffix Array

144


BA9I 
Construct the BurrowsWheeler Transform of a String

300


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

250


BA9K 
Generate the LasttoFirst Mapping of a String

192


BA9L 
Implement BWMatching

197


BA9M 
Implement BetterBWMatching

177


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

177


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

143


BA9P 
Implement TreeColoring

76


BA9Q 
Construct the Partial Suffix Array of a String

139


BA9R 
Construct a Suffix Tree from a Suffix Array

107

