BA10A 
Compute the Probability of a Hidden Path

787


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

647


BA10C 
Implement the Viterbi Algorithm

514


BA10D 
Compute the Probability of a String Emitted by an HMM

329


BA10E 
Construct a Profile HMM

186


BA10F 
Construct a Profile HMM with Pseudocounts

177


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

98


BA10H 
Estimate the Parameters of an HMM

158


BA10I 
Implement Viterbi Learning

124


BA10J 
Solve the Soft Decoding Problem

137


BA10K 
Implement BaumWelch Learning

138


BA11A 
Construct the Graph of a Spectrum

177


BA11B 
Implement DecodingIdealSpectrum

129


BA11C 
Convert a Peptide into a Peptide Vector

182


BA11D 
Convert a Peptide Vector into a Peptide

175


BA11E 
Sequence a Peptide

104


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

104


BA11G 
Implement PSMSearch

97


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

65


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

2618


BA1B 
Find the Most Frequent Words in a String

2721


BA1C 
Find the Reverse Complement of a String

2597


BA1D 
Find All Occurrences of a Pattern in a String

2481


BA1E 
Find Patterns Forming Clumps in a String

2119


BA1F 
Find a Position in a Genome Minimizing the Skew

2100


BA1G 
Compute the Hamming Distance Between Two Strings

2176


BA1H 
Find All Approximate Occurrences of a Pattern in a String

1659


BA1I 
Find the Most Frequent Words with Mismatches in a String

1333


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

1208


BA1K 
Generate the Frequency Array of a String

1081


BA1L 
Implement PatternToNumber

1296


BA1M 
Implement NumberToPattern

1245


BA1N 
Generate the dNeighborhood of a String

1117


BA2A 
Implement MotifEnumeration

1122


BA2B 
Find a Median String

1168


BA2C 
Find a Profilemost Probable kmer in a String

1029


BA2D 
Implement GreedyMotifSearch

946


BA2E 
Implement GreedyMotifSearch with Pseudocounts

828


BA2F 
Implement RandomizedMotifSearch

795


BA2G 
Implement GibbsSampler

607


BA2H 
Implement DistanceBetweenPatternAndStrings

890


BA3A 
Generate the kmer Composition of a String

1217


BA3B 
Reconstruct a String from its Genome Path

1138


BA3C 
Construct the Overlap Graph of a Collection of kmers

1047


BA3D 
Construct the De Bruijn Graph of a String

1032


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

931


BA3F 
Find an Eulerian Cycle in a Graph

731


BA3G 
Find an Eulerian Path in a Graph

674


BA3H 
Reconstruct a String from its kmer Composition

767


BA3I 
Find a kUniversal Circular String

546


BA3J 
Reconstruct a String from its Paired Composition

558


BA3K 
Generate Contigs from a Collection of Reads

417


BA3L 
Construct a String Spelled by a Gapped Genome Path

406


BA3M 
Generate All Maximal NonBranching Paths in a Graph

310


BA4A 
Translate an RNA String into an Amino Acid String

816


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

738


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

654


BA4D 
Compute the Number of Peptides of Given Total Mass

512


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

528


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

413


BA4G 
Implement LeaderboardCyclopeptideSequencing

412


BA4H 
Generate the Convolution of a Spectrum

393


BA4I 
Implement ConvolutionCyclopeptideSequencing

269


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

384


BA4K 
Compute the Score of a Linear Peptide

331


BA4L 
Trim a Peptide Leaderboard

299


BA4M 
Solve the Turnpike Problem

172


BA5A 
Find the Minimum Number of Coins Needed to Make Change

866


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

736


BA5C 
Find a Longest Common Subsequence of Two Strings

826


BA5D 
Find the Longest Path in a DAG

533


BA5E 
Find a HighestScoring Alignment of Two Strings

766


BA5F 
Find a HighestScoring Local Alignment of Two Strings

634


BA5G 
Compute the Edit Distance Between Two Strings

661


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

448


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

391


BA5J 
Align Two Strings Using Affine Gap Penalties

540


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

288


BA5L 
Align Two Strings Using Linear Space

249


BA5M 
Find a HighestScoring Multiple Sequence Alignment

288


BA5N 
Find a Topological Ordering of a DAG

258


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

463


BA6B 
Compute the Number of Breakpoints in a Permutation

495


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

341


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

201


BA6E 
Find All Shared kmers of a Pair of Strings

269


BA6F 
Implement ChromosomeToCycle

225


BA6G 
Implement CycleToChromosome

220


BA6H 
Implement ColoredEdges

198


BA6I 
Implement GraphToGenome

170


BA6J 
Implement 2BreakOnGenomeGraph

171


BA6K 
Implement 2BreakOnGenome

145


BA7A 
Compute Distances Between Leaves

270


BA7B 
Compute Limb Lengths in a Tree

312


BA7C 
Implement AdditivePhylogeny

300


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

199


BA8B 
Compute the Squared Error Distortion

202


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

231


BA8D 
Implement the Soft kMeans Clustering Algorithm

156


BA8E 
Implement Hierarchical Clustering

162


BA9A 
Construct a Trie from a Collection of Patterns

363


BA9B 
Implement TrieMatching

364


BA9C 
Construct the Suffix Tree of a String

271


BA9D 
Find the Longest Repeat in a String

376


BA9E 
Find the Longest Substring Shared by Two Strings

271


BA9F 
Find the Shortest NonShared Substring of Two Strings

225


BA9G 
Construct the Suffix Array of a String

336


BA9H 
Pattern Matching with the Suffix Array

270


BA9I 
Construct the BurrowsWheeler Transform of a String

380


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

326


BA9K 
Generate the LasttoFirst Mapping of a String

269


BA9L 
Implement BWMatching

241


BA9M 
Implement BetterBWMatching

207


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

216


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

213


BA9P 
Implement TreeColoring

100


BA9Q 
Construct the Partial Suffix Array of a String

170


BA9R 
Construct a Suffix Tree from a Suffix Array

124

