BA10A 
Compute the Probability of a Hidden Path

526


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

442


BA10C 
Implement the Viterbi Algorithm

265


BA10D 
Compute the Probability of a String Emitted by an HMM

226


BA10E 
Construct a Profile HMM

138


BA10F 
Construct a Profile HMM with Pseudocounts

127


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

72


BA10H 
Estimate the Parameters of an HMM

98


BA10I 
Implement Viterbi Learning

84


BA10J 
Solve the Soft Decoding Problem

91


BA10K 
Implement BaumWelch Learning

71


BA11A 
Construct the Graph of a Spectrum

121


BA11B 
Implement DecodingIdealSpectrum

91


BA11C 
Convert a Peptide into a Peptide Vector

125


BA11D 
Convert a Peptide Vector into a Peptide

120


BA11E 
Sequence a Peptide

73


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

72


BA11G 
Implement PSMSearch

70


BA11H 
Compute the Size of a Spectral Dictionary

60


BA11I 
Compute the Probability of a Spectral Dictionary

59


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

46


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

1295


BA1B 
Find the Most Frequent Words in a String

1464


BA1C 
Find the Reverse Complement of a String

1420


BA1D 
Find All Occurrences of a Pattern in a String

1316


BA1E 
Find Patterns Forming Clumps in a String

1035


BA1F 
Find a Position in a Genome Minimizing the Skew

1050


BA1G 
Compute the Hamming Distance Between Two Strings

1102


BA1H 
Find All Approximate Occurrences of a Pattern in a String

914


BA1I 
Find the Most Frequent Words with Mismatches in a String

752


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

686


BA1K 
Generate the Frequency Array of a String

636


BA1L 
Implement PatternToNumber

688


BA1M 
Implement NumberToPattern

653


BA1N 
Generate the dNeighborhood of a String

665


BA2A 
Implement MotifEnumeration

556


BA2B 
Find a Median String

562


BA2C 
Find a Profilemost Probable kmer in a String

569


BA2D 
Implement GreedyMotifSearch

478


BA2E 
Implement GreedyMotifSearch with Pseudocounts

417


BA2F 
Implement RandomizedMotifSearch

338


BA2G 
Implement GibbsSampler

293


BA2H 
Implement DistanceBetweenPatternAndStrings

383


BA3A 
Generate the kmer Composition of a String

690


BA3B 
Reconstruct a String from its Genome Path

615


BA3C 
Construct the Overlap Graph of a Collection of kmers

576


BA3D 
Construct the De Bruijn Graph of a String

602


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

527


BA3F 
Find an Eulerian Cycle in a Graph

395


BA3G 
Find an Eulerian Path in a Graph

334


BA3H 
Reconstruct a String from its kmer Composition

359


BA3I 
Find a kUniversal Circular String

263


BA3J 
Reconstruct a String from its Paired Composition

227


BA3K 
Generate Contigs from a Collection of Reads

232


BA3L 
Construct a String Spelled by a Gapped Genome Path

190


BA3M 
Generate All Maximal NonBranching Paths in a Graph

182


BA4A 
Translate an RNA String into an Amino Acid String

457


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

367


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

354


BA4D 
Compute the Number of Peptides of Given Total Mass

230


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

264


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

215


BA4G 
Implement LeaderboardCyclopeptideSequencing

199


BA4H 
Generate the Convolution of a Spectrum

203


BA4I 
Implement ConvolutionCyclopeptideSequencing

142


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

224


BA4K 
Compute the Score of a Linear Peptide

175


BA4L 
Trim a Peptide Leaderboard

157


BA4M 
Solve the Turnpike Problem

84


BA5A 
Find the Minimum Number of Coins Needed to Make Change

550


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

438


BA5C 
Find a Longest Common Subsequence of Two Strings

544


BA5D 
Find the Longest Path in a DAG

351


BA5E 
Find a HighestScoring Alignment of Two Strings

526


BA5F 
Find a HighestScoring Local Alignment of Two Strings

416


BA5G 
Compute the Edit Distance Between Two Strings

473


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

300


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

267


BA5J 
Align Two Strings Using Affine Gap Penalties

311


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

192


BA5L 
Align Two Strings Using Linear Space

173


BA5M 
Find a HighestScoring Multiple Sequence Alignment

203


BA5N 
Find a Topological Ordering of a DAG

141


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

320


BA6B 
Compute the Number of Breakpoints in a Permutation

353


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

236


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

81


BA6E 
Find All Shared kmers of a Pair of Strings

216


BA6F 
Implement ChromosomeToCycle

137


BA6G 
Implement CycleToChromosome

132


BA6H 
Implement ColoredEdges

121


BA6I 
Implement GraphToGenome

99


BA6J 
Implement 2BreakOnGenomeGraph

98


BA6K 
Implement 2BreakOnGenome

93


BA7A 
Compute Distances Between Leaves

178


BA7B 
Compute Limb Lengths in a Tree

185


BA7C 
Implement AdditivePhylogeny

147


BA7D 
Implement UPGMA

135


BA7E 
Implement the Neighbor Joining Algorithm

112


BA7F 
Implement SmallParsimony

94


BA7G 
Adapt SmallParsimony to Unrooted Trees

61


BA8A 
Implement FarthestFirstTraversal

126


BA8B 
Compute the Squared Error Distortion

117


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

132


BA8D 
Implement the Soft kMeans Clustering Algorithm

102


BA8E 
Implement Hierarchical Clustering

98


BA9A 
Construct a Trie from a Collection of Patterns

270


BA9B 
Implement TrieMatching

241


BA9C 
Construct the Suffix Tree of a String

182


BA9D 
Find the Longest Repeat in a String

213


BA9E 
Find the Longest Substring Shared by Two Strings

194


BA9F 
Find the Shortest NonShared Substring of Two Strings

162


BA9G 
Construct the Suffix Array of a String

232


BA9H 
Pattern Matching with the Suffix Array

130


BA9I 
Construct the BurrowsWheeler Transform of a String

275


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

221


BA9K 
Generate the LasttoFirst Mapping of a String

155


BA9L 
Implement BWMatching

172


BA9M 
Implement BetterBWMatching

158


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

165


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

134


BA9P 
Implement TreeColoring

67


BA9Q 
Construct the Partial Suffix Array of a String

131


BA9R 
Construct a Suffix Tree from a Suffix Array

96

