BA10A 
Compute the Probability of a Hidden Path

363


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

312


BA10C 
Implement the Viterbi Algorithm

191


BA10D 
Compute the Probability of a String Emitted by an HMM

167


BA10E 
Construct a Profile HMM

111


BA10F 
Construct a Profile HMM with Pseudocounts

101


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

48


BA10H 
Estimate the Parameters of an HMM

61


BA10I 
Implement Viterbi Learning

50


BA10J 
Solve the Soft Decoding Problem

53


BA10K 
Implement BaumWelch Learning

39


BA11A 
Construct the Graph of a Spectrum

85


BA11B 
Implement DecodingIdealSpectrum

61


BA11C 
Convert a Peptide into a Peptide Vector

90


BA11D 
Convert a Peptide Vector into a Peptide

84


BA11E 
Sequence a Peptide

48


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

50


BA11G 
Implement PSMSearch

49


BA11H 
Compute the Size of a Spectral Dictionary

40


BA11I 
Compute the Probability of a Spectral Dictionary

40


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

32


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

763


BA1B 
Find the Most Frequent Words in a String

917


BA1C 
Find the Reverse Complement of a String

871


BA1D 
Find All Occurrences of a Pattern in a String

789


BA1E 
Find Patterns Forming Clumps in a String

597


BA1F 
Find a Position in a Genome Minimizing the Skew

603


BA1G 
Compute the Hamming Distance Between Two Strings

663


BA1H 
Find All Approximate Occurrences of a Pattern in a String

575


BA1I 
Find the Most Frequent Words with Mismatches in a String

461


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

412


BA1K 
Generate the Frequency Array of a String

375


BA1L 
Implement PatternToNumber

418


BA1M 
Implement NumberToPattern

383


BA1N 
Generate the dNeighborhood of a String

423


BA2A 
Implement MotifEnumeration

350


BA2B 
Find a Median String

334


BA2C 
Find a Profilemost Probable kmer in a String

354


BA2D 
Implement GreedyMotifSearch

283


BA2E 
Implement GreedyMotifSearch with Pseudocounts

234


BA2F 
Implement RandomizedMotifSearch

192


BA2G 
Implement GibbsSampler

178


BA2H 
Implement DistanceBetweenPatternAndStrings

221


BA3A 
Generate the kmer Composition of a String

423


BA3B 
Reconstruct a String from its Genome Path

394


BA3C 
Construct the Overlap Graph of a Collection of kmers

339


BA3D 
Construct the De Bruijn Graph of a String

362


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

329


BA3F 
Find an Eulerian Cycle in a Graph

253


BA3G 
Find an Eulerian Path in a Graph

205


BA3H 
Reconstruct a String from its kmer Composition

202


BA3I 
Find a kUniversal Circular String

154


BA3J 
Reconstruct a String from its Paired Composition

149


BA3K 
Generate Contigs from a Collection of Reads

153


BA3L 
Construct a String Spelled by a Gapped Genome Path

122


BA3M 
Generate All Maximal NonBranching Paths in a Graph

104


BA4A 
Translate an RNA String into an Amino Acid String

292


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

205


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

203


BA4D 
Compute the Number of Peptides of Given Total Mass

112


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

144


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

117


BA4G 
Implement LeaderboardCyclopeptideSequencing

113


BA4H 
Generate the Convolution of a Spectrum

115


BA4I 
Implement ConvolutionCyclopeptideSequencing

83


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

119


BA4K 
Compute the Score of a Linear Peptide

102


BA4L 
Trim a Peptide Leaderboard

88


BA4M 
Solve the Turnpike Problem

58


BA5A 
Find the Minimum Number of Coins Needed to Make Change

427


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

349


BA5C 
Find a Longest Common Subsequence of Two Strings

431


BA5D 
Find the Longest Path in a DAG

284


BA5E 
Find a HighestScoring Alignment of Two Strings

379


BA5F 
Find a HighestScoring Local Alignment of Two Strings

323


BA5G 
Compute the Edit Distance Between Two Strings

393


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

238


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

222


BA5J 
Align Two Strings Using Affine Gap Penalties

241


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

157


BA5L 
Align Two Strings Using Linear Space

137


BA5M 
Find a HighestScoring Multiple Sequence Alignment

162


BA5N 
Find a Topological Ordering of a DAG

99


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

251


BA6B 
Compute the Number of Breakpoints in a Permutation

274


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

175


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

49


BA6E 
Find All Shared kmers of a Pair of Strings

188


BA6F 
Implement ChromosomeToCycle

107


BA6G 
Implement CycleToChromosome

102


BA6H 
Implement ColoredEdges

92


BA6I 
Implement GraphToGenome

76


BA6J 
Implement 2BreakOnGenomeGraph

70


BA6K 
Implement 2BreakOnGenome

57


BA7A 
Compute Distances Between Leaves

115


BA7B 
Compute Limb Lengths in a Tree

120


BA7C 
Implement AdditivePhylogeny

83


BA7D 
Implement UPGMA

78


BA7E 
Implement the Neighbor Joining Algorithm

64


BA7F 
Implement SmallParsimony

52


BA7G 
Adapt SmallParsimony to Unrooted Trees

34


BA8A 
Implement FarthestFirstTraversal

87


BA8B 
Compute the Squared Error Distortion

84


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

83


BA8D 
Implement the Soft kMeans Clustering Algorithm

72


BA8E 
Implement Hierarchical Clustering

70


BA9A 
Construct a Trie from a Collection of Patterns

213


BA9B 
Implement TrieMatching

189


BA9C 
Construct the Suffix Tree of a String

147


BA9D 
Find the Longest Repeat in a String

173


BA9E 
Find the Longest Substring Shared by Two Strings

162


BA9F 
Find the Shortest NonShared Substring of Two Strings

130


BA9G 
Construct the Suffix Array of a String

174


BA9H 
Pattern Matching with the Suffix Array

89


BA9I 
Construct the BurrowsWheeler Transform of a String

203


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

169


BA9K 
Generate the LasttoFirst Mapping of a String

93


BA9L 
Implement BWMatching

129


BA9M 
Implement BetterBWMatching

117


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

128


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

101


BA9P 
Implement TreeColoring

46


BA9Q 
Construct the Partial Suffix Array of a String

103


BA9R 
Construct a Suffix Tree from a Suffix Array

76

