BA10A 
Compute the Probability of a Hidden Path

431


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

364


BA10C 
Implement the Viterbi Algorithm

223


BA10D 
Compute the Probability of a String Emitted by an HMM

197


BA10E 
Construct a Profile HMM

124


BA10F 
Construct a Profile HMM with Pseudocounts

115


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

60


BA10H 
Estimate the Parameters of an HMM

79


BA10I 
Implement Viterbi Learning

71


BA10J 
Solve the Soft Decoding Problem

71


BA10K 
Implement BaumWelch Learning

57


BA11A 
Construct the Graph of a Spectrum

103


BA11B 
Implement DecodingIdealSpectrum

75


BA11C 
Convert a Peptide into a Peptide Vector

109


BA11D 
Convert a Peptide Vector into a Peptide

103


BA11E 
Sequence a Peptide

62


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

63


BA11G 
Implement PSMSearch

62


BA11H 
Compute the Size of a Spectral Dictionary

52


BA11I 
Compute the Probability of a Spectral Dictionary

53


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

42


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

941


BA1B 
Find the Most Frequent Words in a String

1103


BA1C 
Find the Reverse Complement of a String

1063


BA1D 
Find All Occurrences of a Pattern in a String

962


BA1E 
Find Patterns Forming Clumps in a String

753


BA1F 
Find a Position in a Genome Minimizing the Skew

727


BA1G 
Compute the Hamming Distance Between Two Strings

804


BA1H 
Find All Approximate Occurrences of a Pattern in a String

687


BA1I 
Find the Most Frequent Words with Mismatches in a String

552


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

497


BA1K 
Generate the Frequency Array of a String

460


BA1L 
Implement PatternToNumber

516


BA1M 
Implement NumberToPattern

481


BA1N 
Generate the dNeighborhood of a String

503


BA2A 
Implement MotifEnumeration

412


BA2B 
Find a Median String

411


BA2C 
Find a Profilemost Probable kmer in a String

433


BA2D 
Implement GreedyMotifSearch

359


BA2E 
Implement GreedyMotifSearch with Pseudocounts

303


BA2F 
Implement RandomizedMotifSearch

245


BA2G 
Implement GibbsSampler

222


BA2H 
Implement DistanceBetweenPatternAndStrings

285


BA3A 
Generate the kmer Composition of a String

516


BA3B 
Reconstruct a String from its Genome Path

473


BA3C 
Construct the Overlap Graph of a Collection of kmers

421


BA3D 
Construct the De Bruijn Graph of a String

437


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

407


BA3F 
Find an Eulerian Cycle in a Graph

298


BA3G 
Find an Eulerian Path in a Graph

250


BA3H 
Reconstruct a String from its kmer Composition

247


BA3I 
Find a kUniversal Circular String

193


BA3J 
Reconstruct a String from its Paired Composition

178


BA3K 
Generate Contigs from a Collection of Reads

173


BA3L 
Construct a String Spelled by a Gapped Genome Path

144


BA3M 
Generate All Maximal NonBranching Paths in a Graph

127


BA4A 
Translate an RNA String into an Amino Acid String

353


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

261


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

261


BA4D 
Compute the Number of Peptides of Given Total Mass

152


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

191


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

157


BA4G 
Implement LeaderboardCyclopeptideSequencing

148


BA4H 
Generate the Convolution of a Spectrum

153


BA4I 
Implement ConvolutionCyclopeptideSequencing

110


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

174


BA4K 
Compute the Score of a Linear Peptide

135


BA4L 
Trim a Peptide Leaderboard

119


BA4M 
Solve the Turnpike Problem

70


BA5A 
Find the Minimum Number of Coins Needed to Make Change

469


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

379


BA5C 
Find a Longest Common Subsequence of Two Strings

470


BA5D 
Find the Longest Path in a DAG

310


BA5E 
Find a HighestScoring Alignment of Two Strings

424


BA5F 
Find a HighestScoring Local Alignment of Two Strings

346


BA5G 
Compute the Edit Distance Between Two Strings

419


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

264


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

241


BA5J 
Align Two Strings Using Affine Gap Penalties

256


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

170


BA5L 
Align Two Strings Using Linear Space

149


BA5M 
Find a HighestScoring Multiple Sequence Alignment

171


BA5N 
Find a Topological Ordering of a DAG

116


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

272


BA6B 
Compute the Number of Breakpoints in a Permutation

297


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

196


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

59


BA6E 
Find All Shared kmers of a Pair of Strings

202


BA6F 
Implement ChromosomeToCycle

118


BA6G 
Implement CycleToChromosome

113


BA6H 
Implement ColoredEdges

103


BA6I 
Implement GraphToGenome

84


BA6J 
Implement 2BreakOnGenomeGraph

78


BA6K 
Implement 2BreakOnGenome

68


BA7A 
Compute Distances Between Leaves

135


BA7B 
Compute Limb Lengths in a Tree

143


BA7C 
Implement AdditivePhylogeny

96


BA7D 
Implement UPGMA

93


BA7E 
Implement the Neighbor Joining Algorithm

80


BA7F 
Implement SmallParsimony

70


BA7G 
Adapt SmallParsimony to Unrooted Trees

45


BA8A 
Implement FarthestFirstTraversal

101


BA8B 
Compute the Squared Error Distortion

97


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

104


BA8D 
Implement the Soft kMeans Clustering Algorithm

85


BA8E 
Implement Hierarchical Clustering

81


BA9A 
Construct a Trie from a Collection of Patterns

235


BA9B 
Implement TrieMatching

207


BA9C 
Construct the Suffix Tree of a String

160


BA9D 
Find the Longest Repeat in a String

187


BA9E 
Find the Longest Substring Shared by Two Strings

177


BA9F 
Find the Shortest NonShared Substring of Two Strings

141


BA9G 
Construct the Suffix Array of a String

186


BA9H 
Pattern Matching with the Suffix Array

100


BA9I 
Construct the BurrowsWheeler Transform of a String

221


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

184


BA9K 
Generate the LasttoFirst Mapping of a String

113


BA9L 
Implement BWMatching

143


BA9M 
Implement BetterBWMatching

129


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

141


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

112


BA9P 
Implement TreeColoring

56


BA9Q 
Construct the Partial Suffix Array of a String

114


BA9R 
Construct a Suffix Tree from a Suffix Array

86

