BA10A 
Compute the Probability of a Hidden Path

507


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

430


BA10C 
Implement the Viterbi Algorithm

260


BA10D 
Compute the Probability of a String Emitted by an HMM

220


BA10E 
Construct a Profile HMM

135


BA10F 
Construct a Profile HMM with Pseudocounts

124


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

69


BA10H 
Estimate the Parameters of an HMM

93


BA10I 
Implement Viterbi Learning

79


BA10J 
Solve the Soft Decoding Problem

85


BA10K 
Implement BaumWelch Learning

67


BA11A 
Construct the Graph of a Spectrum

116


BA11B 
Implement DecodingIdealSpectrum

88


BA11C 
Convert a Peptide into a Peptide Vector

121


BA11D 
Convert a Peptide Vector into a Peptide

116


BA11E 
Sequence a Peptide

71


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

70


BA11G 
Implement PSMSearch

68


BA11H 
Compute the Size of a Spectral Dictionary

58


BA11I 
Compute the Probability of a Spectral Dictionary

57


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

45


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

1243


BA1B 
Find the Most Frequent Words in a String

1410


BA1C 
Find the Reverse Complement of a String

1373


BA1D 
Find All Occurrences of a Pattern in a String

1270


BA1E 
Find Patterns Forming Clumps in a String

995


BA1F 
Find a Position in a Genome Minimizing the Skew

1010


BA1G 
Compute the Hamming Distance Between Two Strings

1054


BA1H 
Find All Approximate Occurrences of a Pattern in a String

881


BA1I 
Find the Most Frequent Words with Mismatches in a String

725


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

662


BA1K 
Generate the Frequency Array of a String

613


BA1L 
Implement PatternToNumber

664


BA1M 
Implement NumberToPattern

631


BA1N 
Generate the dNeighborhood of a String

639


BA2A 
Implement MotifEnumeration

533


BA2B 
Find a Median String

544


BA2C 
Find a Profilemost Probable kmer in a String

554


BA2D 
Implement GreedyMotifSearch

466


BA2E 
Implement GreedyMotifSearch with Pseudocounts

407


BA2F 
Implement RandomizedMotifSearch

327


BA2G 
Implement GibbsSampler

280


BA2H 
Implement DistanceBetweenPatternAndStrings

371


BA3A 
Generate the kmer Composition of a String

666


BA3B 
Reconstruct a String from its Genome Path

595


BA3C 
Construct the Overlap Graph of a Collection of kmers

560


BA3D 
Construct the De Bruijn Graph of a String

569


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

495


BA3F 
Find an Eulerian Cycle in a Graph

383


BA3G 
Find an Eulerian Path in a Graph

325


BA3H 
Reconstruct a String from its kmer Composition

348


BA3I 
Find a kUniversal Circular String

253


BA3J 
Reconstruct a String from its Paired Composition

219


BA3K 
Generate Contigs from a Collection of Reads

224


BA3L 
Construct a String Spelled by a Gapped Genome Path

184


BA3M 
Generate All Maximal NonBranching Paths in a Graph

175


BA4A 
Translate an RNA String into an Amino Acid String

443


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

356


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

338


BA4D 
Compute the Number of Peptides of Given Total Mass

223


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

254


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

206


BA4G 
Implement LeaderboardCyclopeptideSequencing

191


BA4H 
Generate the Convolution of a Spectrum

195


BA4I 
Implement ConvolutionCyclopeptideSequencing

136


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

213


BA4K 
Compute the Score of a Linear Peptide

167


BA4L 
Trim a Peptide Leaderboard

151


BA4M 
Solve the Turnpike Problem

81


BA5A 
Find the Minimum Number of Coins Needed to Make Change

537


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

427


BA5C 
Find a Longest Common Subsequence of Two Strings

535


BA5D 
Find the Longest Path in a DAG

344


BA5E 
Find a HighestScoring Alignment of Two Strings

518


BA5F 
Find a HighestScoring Local Alignment of Two Strings

411


BA5G 
Compute the Edit Distance Between Two Strings

467


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

293


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

262


BA5J 
Align Two Strings Using Affine Gap Penalties

305


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

189


BA5L 
Align Two Strings Using Linear Space

168


BA5M 
Find a HighestScoring Multiple Sequence Alignment

199


BA5N 
Find a Topological Ordering of a DAG

135


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

317


BA6B 
Compute the Number of Breakpoints in a Permutation

350


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

233


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

79


BA6E 
Find All Shared kmers of a Pair of Strings

214


BA6F 
Implement ChromosomeToCycle

133


BA6G 
Implement CycleToChromosome

129


BA6H 
Implement ColoredEdges

118


BA6I 
Implement GraphToGenome

96


BA6J 
Implement 2BreakOnGenomeGraph

95


BA6K 
Implement 2BreakOnGenome

91


BA7A 
Compute Distances Between Leaves

170


BA7B 
Compute Limb Lengths in a Tree

173


BA7C 
Implement AdditivePhylogeny

138


BA7D 
Implement UPGMA

130


BA7E 
Implement the Neighbor Joining Algorithm

106


BA7F 
Implement SmallParsimony

88


BA7G 
Adapt SmallParsimony to Unrooted Trees

57


BA8A 
Implement FarthestFirstTraversal

121


BA8B 
Compute the Squared Error Distortion

112


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

125


BA8D 
Implement the Soft kMeans Clustering Algorithm

100


BA8E 
Implement Hierarchical Clustering

96


BA9A 
Construct a Trie from a Collection of Patterns

264


BA9B 
Implement TrieMatching

237


BA9C 
Construct the Suffix Tree of a String

180


BA9D 
Find the Longest Repeat in a String

209


BA9E 
Find the Longest Substring Shared by Two Strings

191


BA9F 
Find the Shortest NonShared Substring of Two Strings

158


BA9G 
Construct the Suffix Array of a String

222


BA9H 
Pattern Matching with the Suffix Array

126


BA9I 
Construct the BurrowsWheeler Transform of a String

268


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

215


BA9K 
Generate the LasttoFirst Mapping of a String

145


BA9L 
Implement BWMatching

168


BA9M 
Implement BetterBWMatching

153


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

161


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

131


BA9P 
Implement TreeColoring

65


BA9Q 
Construct the Partial Suffix Array of a String

128


BA9R 
Construct a Suffix Tree from a Suffix Array

94

