BA10A 
Compute the Probability of a Hidden Path

571


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

477


BA10C 
Implement the Viterbi Algorithm

279


BA10D 
Compute the Probability of a String Emitted by an HMM

237


BA10E 
Construct a Profile HMM

147


BA10F 
Construct a Profile HMM with Pseudocounts

134


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

76


BA10H 
Estimate the Parameters of an HMM

102


BA10I 
Implement Viterbi Learning

87


BA10J 
Solve the Soft Decoding Problem

94


BA10K 
Implement BaumWelch Learning

74


BA11A 
Construct the Graph of a Spectrum

132


BA11B 
Implement DecodingIdealSpectrum

96


BA11C 
Convert a Peptide into a Peptide Vector

136


BA11D 
Convert a Peptide Vector into a Peptide

131


BA11E 
Sequence a Peptide

78


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

78


BA11G 
Implement PSMSearch

75


BA11H 
Compute the Size of a Spectral Dictionary

66


BA11I 
Compute the Probability of a Spectral Dictionary

65


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

51


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

1449


BA1B 
Find the Most Frequent Words in a String

1614


BA1C 
Find the Reverse Complement of a String

1549


BA1D 
Find All Occurrences of a Pattern in a String

1442


BA1E 
Find Patterns Forming Clumps in a String

1145


BA1F 
Find a Position in a Genome Minimizing the Skew

1154


BA1G 
Compute the Hamming Distance Between Two Strings

1217


BA1H 
Find All Approximate Occurrences of a Pattern in a String

1017


BA1I 
Find the Most Frequent Words with Mismatches in a String

829


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

755


BA1K 
Generate the Frequency Array of a String

692


BA1L 
Implement PatternToNumber

750


BA1M 
Implement NumberToPattern

716


BA1N 
Generate the dNeighborhood of a String

723


BA2A 
Implement MotifEnumeration

602


BA2B 
Find a Median String

608


BA2C 
Find a Profilemost Probable kmer in a String

613


BA2D 
Implement GreedyMotifSearch

521


BA2E 
Implement GreedyMotifSearch with Pseudocounts

459


BA2F 
Implement RandomizedMotifSearch

375


BA2G 
Implement GibbsSampler

324


BA2H 
Implement DistanceBetweenPatternAndStrings

410


BA3A 
Generate the kmer Composition of a String

750


BA3B 
Reconstruct a String from its Genome Path

673


BA3C 
Construct the Overlap Graph of a Collection of kmers

625


BA3D 
Construct the De Bruijn Graph of a String

645


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

565


BA3F 
Find an Eulerian Cycle in a Graph

430


BA3G 
Find an Eulerian Path in a Graph

364


BA3H 
Reconstruct a String from its kmer Composition

394


BA3I 
Find a kUniversal Circular String

290


BA3J 
Reconstruct a String from its Paired Composition

251


BA3K 
Generate Contigs from a Collection of Reads

247


BA3L 
Construct a String Spelled by a Gapped Genome Path

207


BA3M 
Generate All Maximal NonBranching Paths in a Graph

193


BA4A 
Translate an RNA String into an Amino Acid String

503


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

398


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

382


BA4D 
Compute the Number of Peptides of Given Total Mass

252


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

293


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

237


BA4G 
Implement LeaderboardCyclopeptideSequencing

216


BA4H 
Generate the Convolution of a Spectrum

226


BA4I 
Implement ConvolutionCyclopeptideSequencing

155


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

245


BA4K 
Compute the Score of a Linear Peptide

195


BA4L 
Trim a Peptide Leaderboard

173


BA4M 
Solve the Turnpike Problem

93


BA5A 
Find the Minimum Number of Coins Needed to Make Change

574


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

456


BA5C 
Find a Longest Common Subsequence of Two Strings

564


BA5D 
Find the Longest Path in a DAG

369


BA5E 
Find a HighestScoring Alignment of Two Strings

541


BA5F 
Find a HighestScoring Local Alignment of Two Strings

429


BA5G 
Compute the Edit Distance Between Two Strings

490


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

312


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

275


BA5J 
Align Two Strings Using Affine Gap Penalties

320


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

201


BA5L 
Align Two Strings Using Linear Space

177


BA5M 
Find a HighestScoring Multiple Sequence Alignment

210


BA5N 
Find a Topological Ordering of a DAG

149


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

330


BA6B 
Compute the Number of Breakpoints in a Permutation

365


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

243


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

84


BA6E 
Find All Shared kmers of a Pair of Strings

220


BA6F 
Implement ChromosomeToCycle

142


BA6G 
Implement CycleToChromosome

138


BA6H 
Implement ColoredEdges

127


BA6I 
Implement GraphToGenome

105


BA6J 
Implement 2BreakOnGenomeGraph

105


BA6K 
Implement 2BreakOnGenome

98


BA7A 
Compute Distances Between Leaves

191


BA7B 
Compute Limb Lengths in a Tree

197


BA7C 
Implement AdditivePhylogeny

158


BA7D 
Implement UPGMA

144


BA7E 
Implement the Neighbor Joining Algorithm

121


BA7F 
Implement SmallParsimony

98


BA7G 
Adapt SmallParsimony to Unrooted Trees

68


BA8A 
Implement FarthestFirstTraversal

135


BA8B 
Compute the Squared Error Distortion

129


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

139


BA8D 
Implement the Soft kMeans Clustering Algorithm

106


BA8E 
Implement Hierarchical Clustering

105


BA9A 
Construct a Trie from a Collection of Patterns

278


BA9B 
Implement TrieMatching

251


BA9C 
Construct the Suffix Tree of a String

189


BA9D 
Find the Longest Repeat in a String

221


BA9E 
Find the Longest Substring Shared by Two Strings

200


BA9F 
Find the Shortest NonShared Substring of Two Strings

169


BA9G 
Construct the Suffix Array of a String

240


BA9H 
Pattern Matching with the Suffix Array

136


BA9I 
Construct the BurrowsWheeler Transform of a String

283


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

227


BA9K 
Generate the LasttoFirst Mapping of a String

171


BA9L 
Implement BWMatching

178


BA9M 
Implement BetterBWMatching

162


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

169


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

137


BA9P 
Implement TreeColoring

71


BA9Q 
Construct the Partial Suffix Array of a String

134


BA9R 
Construct a Suffix Tree from a Suffix Array

101

