BA10A 
Compute the Probability of a Hidden Path

807


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

662


BA10C 
Implement the Viterbi Algorithm

528


BA10D 
Compute the Probability of a String Emitted by an HMM

333


BA10E 
Construct a Profile HMM

188


BA10F 
Construct a Profile HMM with Pseudocounts

180


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

99


BA10H 
Estimate the Parameters of an HMM

159


BA10I 
Implement Viterbi Learning

124


BA10J 
Solve the Soft Decoding Problem

137


BA10K 
Implement BaumWelch Learning

138


BA11A 
Construct the Graph of a Spectrum

179


BA11B 
Implement DecodingIdealSpectrum

132


BA11C 
Convert a Peptide into a Peptide Vector

189


BA11D 
Convert a Peptide Vector into a Peptide

180


BA11E 
Sequence a Peptide

106


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

106


BA11G 
Implement PSMSearch

99


BA11H 
Compute the Size of a Spectral Dictionary

91


BA11I 
Compute the Probability of a Spectral Dictionary

89


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

66


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

2755


BA1B 
Find the Most Frequent Words in a String

2849


BA1C 
Find the Reverse Complement of a String

2712


BA1D 
Find All Occurrences of a Pattern in a String

2596


BA1E 
Find Patterns Forming Clumps in a String

2231


BA1F 
Find a Position in a Genome Minimizing the Skew

2202


BA1G 
Compute the Hamming Distance Between Two Strings

2272


BA1H 
Find All Approximate Occurrences of a Pattern in a String

1738


BA1I 
Find the Most Frequent Words with Mismatches in a String

1401


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

1269


BA1K 
Generate the Frequency Array of a String

1134


BA1L 
Implement PatternToNumber

1353


BA1M 
Implement NumberToPattern

1303


BA1N 
Generate the dNeighborhood of a String

1177


BA2A 
Implement MotifEnumeration

1173


BA2B 
Find a Median String

1219


BA2C 
Find a Profilemost Probable kmer in a String

1068


BA2D 
Implement GreedyMotifSearch

968


BA2E 
Implement GreedyMotifSearch with Pseudocounts

845


BA2F 
Implement RandomizedMotifSearch

824


BA2G 
Implement GibbsSampler

634


BA2H 
Implement DistanceBetweenPatternAndStrings

925


BA3A 
Generate the kmer Composition of a String

1242


BA3B 
Reconstruct a String from its Genome Path

1161


BA3C 
Construct the Overlap Graph of a Collection of kmers

1071


BA3D 
Construct the De Bruijn Graph of a String

1054


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

954


BA3F 
Find an Eulerian Cycle in a Graph

753


BA3G 
Find an Eulerian Path in a Graph

693


BA3H 
Reconstruct a String from its kmer Composition

783


BA3I 
Find a kUniversal Circular String

558


BA3J 
Reconstruct a String from its Paired Composition

573


BA3K 
Generate Contigs from a Collection of Reads

424


BA3L 
Construct a String Spelled by a Gapped Genome Path

417


BA3M 
Generate All Maximal NonBranching Paths in a Graph

313


BA4A 
Translate an RNA String into an Amino Acid String

852


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

764


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

685


BA4D 
Compute the Number of Peptides of Given Total Mass

542


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

546


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

425


BA4G 
Implement LeaderboardCyclopeptideSequencing

424


BA4H 
Generate the Convolution of a Spectrum

407


BA4I 
Implement ConvolutionCyclopeptideSequencing

275


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

400


BA4K 
Compute the Score of a Linear Peptide

346


BA4L 
Trim a Peptide Leaderboard

313


BA4M 
Solve the Turnpike Problem

174


BA5A 
Find the Minimum Number of Coins Needed to Make Change

891


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

761


BA5C 
Find a Longest Common Subsequence of Two Strings

844


BA5D 
Find the Longest Path in a DAG

544


BA5E 
Find a HighestScoring Alignment of Two Strings

778


BA5F 
Find a HighestScoring Local Alignment of Two Strings

640


BA5G 
Compute the Edit Distance Between Two Strings

670


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

453


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

396


BA5J 
Align Two Strings Using Affine Gap Penalties

548


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

292


BA5L 
Align Two Strings Using Linear Space

253


BA5M 
Find a HighestScoring Multiple Sequence Alignment

293


BA5N 
Find a Topological Ordering of a DAG

266


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

484


BA6B 
Compute the Number of Breakpoints in a Permutation

514


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

356


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

210


BA6E 
Find All Shared kmers of a Pair of Strings

277


BA6F 
Implement ChromosomeToCycle

243


BA6G 
Implement CycleToChromosome

238


BA6H 
Implement ColoredEdges

213


BA6I 
Implement GraphToGenome

183


BA6J 
Implement 2BreakOnGenomeGraph

180


BA6K 
Implement 2BreakOnGenome

149


BA7A 
Compute Distances Between Leaves

273


BA7B 
Compute Limb Lengths in a Tree

315


BA7C 
Implement AdditivePhylogeny

305


BA7D 
Implement UPGMA

213


BA7E 
Implement the Neighbor Joining Algorithm

200


BA7F 
Implement SmallParsimony

143


BA7G 
Adapt SmallParsimony to Unrooted Trees

102


BA8A 
Implement FarthestFirstTraversal

204


BA8B 
Compute the Squared Error Distortion

207


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

236


BA8D 
Implement the Soft kMeans Clustering Algorithm

159


BA8E 
Implement Hierarchical Clustering

165


BA9A 
Construct a Trie from a Collection of Patterns

366


BA9B 
Implement TrieMatching

368


BA9C 
Construct the Suffix Tree of a String

273


BA9D 
Find the Longest Repeat in a String

381


BA9E 
Find the Longest Substring Shared by Two Strings

274


BA9F 
Find the Shortest NonShared Substring of Two Strings

228


BA9G 
Construct the Suffix Array of a String

337


BA9H 
Pattern Matching with the Suffix Array

279


BA9I 
Construct the BurrowsWheeler Transform of a String

383


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

329


BA9K 
Generate the LasttoFirst Mapping of a String

272


BA9L 
Implement BWMatching

244


BA9M 
Implement BetterBWMatching

210


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

221


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

217


BA9P 
Implement TreeColoring

102


BA9Q 
Construct the Partial Suffix Array of a String

172


BA9R 
Construct a Suffix Tree from a Suffix Array

126

