BA10A 
Compute the Probability of a Hidden Path

484


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

408


BA10C 
Implement the Viterbi Algorithm

253


BA10D 
Compute the Probability of a String Emitted by an HMM

217


BA10E 
Construct a Profile HMM

134


BA10F 
Construct a Profile HMM with Pseudocounts

123


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

68


BA10H 
Estimate the Parameters of an HMM

91


BA10I 
Implement Viterbi Learning

79


BA10J 
Solve the Soft Decoding Problem

85


BA10K 
Implement BaumWelch Learning

67


BA11A 
Construct the Graph of a Spectrum

114


BA11B 
Implement DecodingIdealSpectrum

87


BA11C 
Convert a Peptide into a Peptide Vector

119


BA11D 
Convert a Peptide Vector into a Peptide

114


BA11E 
Sequence a Peptide

70


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

69


BA11G 
Implement PSMSearch

67


BA11H 
Compute the Size of a Spectral Dictionary

57


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

1135


BA1B 
Find the Most Frequent Words in a String

1307


BA1C 
Find the Reverse Complement of a String

1268


BA1D 
Find All Occurrences of a Pattern in a String

1174


BA1E 
Find Patterns Forming Clumps in a String

906


BA1F 
Find a Position in a Genome Minimizing the Skew

918


BA1G 
Compute the Hamming Distance Between Two Strings

961


BA1H 
Find All Approximate Occurrences of a Pattern in a String

843


BA1I 
Find the Most Frequent Words with Mismatches in a String

689


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

627


BA1K 
Generate the Frequency Array of a String

585


BA1L 
Implement PatternToNumber

633


BA1M 
Implement NumberToPattern

600


BA1N 
Generate the dNeighborhood of a String

614


BA2A 
Implement MotifEnumeration

504


BA2B 
Find a Median String

515


BA2C 
Find a Profilemost Probable kmer in a String

531


BA2D 
Implement GreedyMotifSearch

442


BA2E 
Implement GreedyMotifSearch with Pseudocounts

383


BA2F 
Implement RandomizedMotifSearch

305


BA2G 
Implement GibbsSampler

265


BA2H 
Implement DistanceBetweenPatternAndStrings

350


BA3A 
Generate the kmer Composition of a String

636


BA3B 
Reconstruct a String from its Genome Path

568


BA3C 
Construct the Overlap Graph of a Collection of kmers

523


BA3D 
Construct the De Bruijn Graph of a String

533


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

478


BA3F 
Find an Eulerian Cycle in a Graph

368


BA3G 
Find an Eulerian Path in a Graph

310


BA3H 
Reconstruct a String from its kmer Composition

313


BA3I 
Find a kUniversal Circular String

234


BA3J 
Reconstruct a String from its Paired Composition

207


BA3K 
Generate Contigs from a Collection of Reads

202


BA3L 
Construct a String Spelled by a Gapped Genome Path

171


BA3M 
Generate All Maximal NonBranching Paths in a Graph

151


BA4A 
Translate an RNA String into an Amino Acid String

430


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

337


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

330


BA4D 
Compute the Number of Peptides of Given Total Mass

210


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

243


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

200


BA4G 
Implement LeaderboardCyclopeptideSequencing

180


BA4H 
Generate the Convolution of a Spectrum

190


BA4I 
Implement ConvolutionCyclopeptideSequencing

132


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

207


BA4K 
Compute the Score of a Linear Peptide

163


BA4L 
Trim a Peptide Leaderboard

147


BA4M 
Solve the Turnpike Problem

80


BA5A 
Find the Minimum Number of Coins Needed to Make Change

522


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

417


BA5C 
Find a Longest Common Subsequence of Two Strings

510


BA5D 
Find the Longest Path in a DAG

337


BA5E 
Find a HighestScoring Alignment of Two Strings

487


BA5F 
Find a HighestScoring Local Alignment of Two Strings

399


BA5G 
Compute the Edit Distance Between Two Strings

459


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

290


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

260


BA5J 
Align Two Strings Using Affine Gap Penalties

288


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

186


BA5L 
Align Two Strings Using Linear Space

164


BA5M 
Find a HighestScoring Multiple Sequence Alignment

183


BA5N 
Find a Topological Ordering of a DAG

129


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

295


BA6B 
Compute the Number of Breakpoints in a Permutation

323


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

210


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

68


BA6E 
Find All Shared kmers of a Pair of Strings

211


BA6F 
Implement ChromosomeToCycle

127


BA6G 
Implement CycleToChromosome

123


BA6H 
Implement ColoredEdges

113


BA6I 
Implement GraphToGenome

93


BA6J 
Implement 2BreakOnGenomeGraph

87


BA6K 
Implement 2BreakOnGenome

81


BA7A 
Compute Distances Between Leaves

152


BA7B 
Compute Limb Lengths in a Tree

158


BA7C 
Implement AdditivePhylogeny

113


BA7D 
Implement UPGMA

111


BA7E 
Implement the Neighbor Joining Algorithm

93


BA7F 
Implement SmallParsimony

83


BA7G 
Adapt SmallParsimony to Unrooted Trees

52


BA8A 
Implement FarthestFirstTraversal

116


BA8B 
Compute the Squared Error Distortion

109


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

122


BA8D 
Implement the Soft kMeans Clustering Algorithm

98


BA8E 
Implement Hierarchical Clustering

94


BA9A 
Construct a Trie from a Collection of Patterns

260


BA9B 
Implement TrieMatching

234


BA9C 
Construct the Suffix Tree of a String

175


BA9D 
Find the Longest Repeat in a String

204


BA9E 
Find the Longest Substring Shared by Two Strings

187


BA9F 
Find the Shortest NonShared Substring of Two Strings

152


BA9G 
Construct the Suffix Array of a String

218


BA9H 
Pattern Matching with the Suffix Array

119


BA9I 
Construct the BurrowsWheeler Transform of a String

264


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

212


BA9K 
Generate the LasttoFirst Mapping of a String

141


BA9L 
Implement BWMatching

164


BA9M 
Implement BetterBWMatching

149


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

157


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

128


BA9P 
Implement TreeColoring

63


BA9Q 
Construct the Partial Suffix Array of a String

125


BA9R 
Construct a Suffix Tree from a Suffix Array

93

