BA10A 
Compute the Probability of a Hidden Path

284


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

240


BA10C 
Implement the Viterbi Algorithm

150


BA10D 
Compute the Probability of a String Emitted by an HMM

134


BA10E 
Construct a Profile HMM

88


BA10F 
Construct a Profile HMM with Pseudocounts

78


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

36


BA10H 
Estimate the Parameters of an HMM

54


BA10I 
Implement Viterbi Learning

43


BA10J 
Solve the Soft Decoding Problem

45


BA10K 
Implement BaumWelch Learning

32


BA11A 
Construct the Graph of a Spectrum

75


BA11B 
Implement DecodingIdealSpectrum

54


BA11C 
Convert a Peptide into a Peptide Vector

81


BA11D 
Convert a Peptide Vector into a Peptide

75


BA11E 
Sequence a Peptide

44


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

46


BA11G 
Implement PSMSearch

44


BA11H 
Compute the Size of a Spectral Dictionary

37


BA11I 
Compute the Probability of a Spectral Dictionary

36


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

27


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

586


BA1B 
Find the Most Frequent Words in a String

752


BA1C 
Find the Reverse Complement of a String

685


BA1D 
Find All Occurrences of a Pattern in a String

639


BA1E 
Find Patterns Forming Clumps in a String

504


BA1F 
Find a Position in a Genome Minimizing the Skew

487


BA1G 
Compute the Hamming Distance Between Two Strings

489


BA1H 
Find All Approximate Occurrences of a Pattern in a String

487


BA1I 
Find the Most Frequent Words with Mismatches in a String

390


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

349


BA1K 
Generate the Frequency Array of a String

309


BA1L 
Implement PatternToNumber

345


BA1M 
Implement NumberToPattern

312


BA1N 
Generate the dNeighborhood of a String

338


BA2A 
Implement MotifEnumeration

287


BA2B 
Find a Median String

252


BA2C 
Find a Profilemost Probable kmer in a String

272


BA2D 
Implement GreedyMotifSearch

227


BA2E 
Implement GreedyMotifSearch with Pseudocounts

192


BA2F 
Implement RandomizedMotifSearch

155


BA2G 
Implement GibbsSampler

143


BA2H 
Implement DistanceBetweenPatternAndStrings

186


BA3A 
Generate the kmer Composition of a String

312


BA3B 
Reconstruct a String from its Genome Path

251


BA3C 
Construct the Overlap Graph of a Collection of kmers

267


BA3D 
Construct the De Bruijn Graph of a String

258


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

241


BA3F 
Find an Eulerian Cycle in a Graph

181


BA3G 
Find an Eulerian Path in a Graph

165


BA3H 
Reconstruct a String from its kmer Composition

159


BA3I 
Find a kUniversal Circular String

128


BA3J 
Reconstruct a String from its Paired Composition

101


BA3K 
Generate Contigs from a Collection of Reads

113


BA3L 
Construct a String Spelled by a Gapped Genome Path

94


BA3M 
Generate All Maximal NonBranching Paths in a Graph

91


BA4A 
Translate an RNA String into an Amino Acid String

222


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

175


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

176


BA4D 
Compute the Number of Peptides of Given Total Mass

98


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

125


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

103


BA4G 
Implement LeaderboardCyclopeptideSequencing

102


BA4H 
Generate the Convolution of a Spectrum

102


BA4I 
Implement ConvolutionCyclopeptideSequencing

71


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

105


BA4K 
Compute the Score of a Linear Peptide

89


BA4L 
Trim a Peptide Leaderboard

78


BA4M 
Solve the Turnpike Problem

49


BA5A 
Find the Minimum Number of Coins Needed to Make Change

393


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

325


BA5C 
Find a Longest Common Subsequence of Two Strings

382


BA5D 
Find the Longest Path in a DAG

262


BA5E 
Find a HighestScoring Alignment of Two Strings

308


BA5F 
Find a HighestScoring Local Alignment of Two Strings

270


BA5G 
Compute the Edit Distance Between Two Strings

323


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

224


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

206


BA5J 
Align Two Strings Using Affine Gap Penalties

192


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

124


BA5L 
Align Two Strings Using Linear Space

107


BA5M 
Find a HighestScoring Multiple Sequence Alignment

130


BA5N 
Find a Topological Ordering of a DAG

80


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

235


BA6B 
Compute the Number of Breakpoints in a Permutation

253


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

163


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

37


BA6E 
Find All Shared kmers of a Pair of Strings

172


BA6F 
Implement ChromosomeToCycle

92


BA6G 
Implement CycleToChromosome

87


BA6H 
Implement ColoredEdges

80


BA6I 
Implement GraphToGenome

64


BA6J 
Implement 2BreakOnGenomeGraph

58


BA6K 
Implement 2BreakOnGenome

43


BA7A 
Compute Distances Between Leaves

101


BA7B 
Compute Limb Lengths in a Tree

92


BA7C 
Implement AdditivePhylogeny

61


BA7D 
Implement UPGMA

56


BA7E 
Implement the Neighbor Joining Algorithm

50


BA7F 
Implement SmallParsimony

44


BA7G 
Adapt SmallParsimony to Unrooted Trees

27


BA8A 
Implement FarthestFirstTraversal

76


BA8B 
Compute the Squared Error Distortion

74


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

67


BA8D 
Implement the Soft kMeans Clustering Algorithm

62


BA8E 
Implement Hierarchical Clustering

60


BA9A 
Construct a Trie from a Collection of Patterns

196


BA9B 
Implement TrieMatching

175


BA9C 
Construct the Suffix Tree of a String

138


BA9D 
Find the Longest Repeat in a String

162


BA9E 
Find the Longest Substring Shared by Two Strings

152


BA9F 
Find the Shortest NonShared Substring of Two Strings

121


BA9G 
Construct the Suffix Array of a String

157


BA9H 
Pattern Matching with the Suffix Array

76


BA9I 
Construct the BurrowsWheeler Transform of a String

180


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

149


BA9K 
Generate the LasttoFirst Mapping of a String

78


BA9L 
Implement BWMatching

114


BA9M 
Implement BetterBWMatching

108


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

119


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

91


BA9P 
Implement TreeColoring

40


BA9Q 
Construct the Partial Suffix Array of a String

94


BA9R 
Construct a Suffix Tree from a Suffix Array

69

