BA10A 
Compute the Probability of a Hidden Path

714


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

595


BA10C 
Implement the Viterbi Algorithm

439


BA10D 
Compute the Probability of a String Emitted by an HMM

306


BA10E 
Construct a Profile HMM

176


BA10F 
Construct a Profile HMM with Pseudocounts

169


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

95


BA10H 
Estimate the Parameters of an HMM

150


BA10I 
Implement Viterbi Learning

115


BA10J 
Solve the Soft Decoding Problem

131


BA10K 
Implement BaumWelch Learning

123


BA11A 
Construct the Graph of a Spectrum

165


BA11B 
Implement DecodingIdealSpectrum

121


BA11C 
Convert a Peptide into a Peptide Vector

171


BA11D 
Convert a Peptide Vector into a Peptide

165


BA11E 
Sequence a Peptide

98


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

98


BA11G 
Implement PSMSearch

91


BA11H 
Compute the Size of a Spectral Dictionary

85


BA11I 
Compute the Probability of a Spectral Dictionary

84


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

63


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

2262


BA1B 
Find the Most Frequent Words in a String

2401


BA1C 
Find the Reverse Complement of a String

2295


BA1D 
Find All Occurrences of a Pattern in a String

2164


BA1E 
Find Patterns Forming Clumps in a String

1865


BA1F 
Find a Position in a Genome Minimizing the Skew

1835


BA1G 
Compute the Hamming Distance Between Two Strings

1908


BA1H 
Find All Approximate Occurrences of a Pattern in a String

1441


BA1I 
Find the Most Frequent Words with Mismatches in a String

1202


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

1087


BA1K 
Generate the Frequency Array of a String

963


BA1L 
Implement PatternToNumber

1154


BA1M 
Implement NumberToPattern

1104


BA1N 
Generate the dNeighborhood of a String

1001


BA2A 
Implement MotifEnumeration

1003


BA2B 
Find a Median String

975


BA2C 
Find a Profilemost Probable kmer in a String

892


BA2D 
Implement GreedyMotifSearch

833


BA2E 
Implement GreedyMotifSearch with Pseudocounts

730


BA2F 
Implement RandomizedMotifSearch

663


BA2G 
Implement GibbsSampler

528


BA2H 
Implement DistanceBetweenPatternAndStrings

781


BA3A 
Generate the kmer Composition of a String

1085


BA3B 
Reconstruct a String from its Genome Path

1012


BA3C 
Construct the Overlap Graph of a Collection of kmers

946


BA3D 
Construct the De Bruijn Graph of a String

930


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

829


BA3F 
Find an Eulerian Cycle in a Graph

642


BA3G 
Find an Eulerian Path in a Graph

580


BA3H 
Reconstruct a String from its kmer Composition

703


BA3I 
Find a kUniversal Circular String

477


BA3J 
Reconstruct a String from its Paired Composition

459


BA3K 
Generate Contigs from a Collection of Reads

379


BA3L 
Construct a String Spelled by a Gapped Genome Path

358


BA3M 
Generate All Maximal NonBranching Paths in a Graph

281


BA4A 
Translate an RNA String into an Amino Acid String

727


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

636


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

572


BA4D 
Compute the Number of Peptides of Given Total Mass

421


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

448


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

356


BA4G 
Implement LeaderboardCyclopeptideSequencing

351


BA4H 
Generate the Convolution of a Spectrum

344


BA4I 
Implement ConvolutionCyclopeptideSequencing

233


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

341


BA4K 
Compute the Score of a Linear Peptide

284


BA4L 
Trim a Peptide Leaderboard

257


BA4M 
Solve the Turnpike Problem

151


BA5A 
Find the Minimum Number of Coins Needed to Make Change

776


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

630


BA5C 
Find a Longest Common Subsequence of Two Strings

755


BA5D 
Find the Longest Path in a DAG

471


BA5E 
Find a HighestScoring Alignment of Two Strings

715


BA5F 
Find a HighestScoring Local Alignment of Two Strings

576


BA5G 
Compute the Edit Distance Between Two Strings

614


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

400


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

358


BA5J 
Align Two Strings Using Affine Gap Penalties

472


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

266


BA5L 
Align Two Strings Using Linear Space

230


BA5M 
Find a HighestScoring Multiple Sequence Alignment

271


BA5N 
Find a Topological Ordering of a DAG

229


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

415


BA6B 
Compute the Number of Breakpoints in a Permutation

470


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

308


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

160


BA6E 
Find All Shared kmers of a Pair of Strings

264


BA6F 
Implement ChromosomeToCycle

205


BA6G 
Implement CycleToChromosome

200


BA6H 
Implement ColoredEdges

183


BA6I 
Implement GraphToGenome

153


BA6J 
Implement 2BreakOnGenomeGraph

158


BA6K 
Implement 2BreakOnGenome

136


BA7A 
Compute Distances Between Leaves

245


BA7B 
Compute Limb Lengths in a Tree

279


BA7C 
Implement AdditivePhylogeny

243


BA7D 
Implement UPGMA

196


BA7E 
Implement the Neighbor Joining Algorithm

184


BA7F 
Implement SmallParsimony

129


BA7G 
Adapt SmallParsimony to Unrooted Trees

94


BA8A 
Implement FarthestFirstTraversal

178


BA8B 
Compute the Squared Error Distortion

179


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

204


BA8D 
Implement the Soft kMeans Clustering Algorithm

141


BA8E 
Implement Hierarchical Clustering

147


BA9A 
Construct a Trie from a Collection of Patterns

348


BA9B 
Implement TrieMatching

352


BA9C 
Construct the Suffix Tree of a String

260


BA9D 
Find the Longest Repeat in a String

321


BA9E 
Find the Longest Substring Shared by Two Strings

260


BA9F 
Find the Shortest NonShared Substring of Two Strings

214


BA9G 
Construct the Suffix Array of a String

321


BA9H 
Pattern Matching with the Suffix Array

231


BA9I 
Construct the BurrowsWheeler Transform of a String

363


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

310


BA9K 
Generate the LasttoFirst Mapping of a String

250


BA9L 
Implement BWMatching

230


BA9M 
Implement BetterBWMatching

202


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

209


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

191


BA9P 
Implement TreeColoring

96


BA9Q 
Construct the Partial Suffix Array of a String

167


BA9R 
Construct a Suffix Tree from a Suffix Array

124

