BA10A 
Compute the Probability of a Hidden Path

435


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

369


BA10C 
Implement the Viterbi Algorithm

229


BA10D 
Compute the Probability of a String Emitted by an HMM

202


BA10E 
Construct a Profile HMM

126


BA10F 
Construct a Profile HMM with Pseudocounts

116


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

61


BA10H 
Estimate the Parameters of an HMM

82


BA10I 
Implement Viterbi Learning

73


BA10J 
Solve the Soft Decoding Problem

73


BA10K 
Implement BaumWelch Learning

59


BA11A 
Construct the Graph of a Spectrum

105


BA11B 
Implement DecodingIdealSpectrum

77


BA11C 
Convert a Peptide into a Peptide Vector

111


BA11D 
Convert a Peptide Vector into a Peptide

105


BA11E 
Sequence a Peptide

63


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

64


BA11G 
Implement PSMSearch

63


BA11H 
Compute the Size of a Spectral Dictionary

52


BA11I 
Compute the Probability of a Spectral Dictionary

53


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

42


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

958


BA1B 
Find the Most Frequent Words in a String

1120


BA1C 
Find the Reverse Complement of a String

1077


BA1D 
Find All Occurrences of a Pattern in a String

976


BA1E 
Find Patterns Forming Clumps in a String

766


BA1F 
Find a Position in a Genome Minimizing the Skew

737


BA1G 
Compute the Hamming Distance Between Two Strings

820


BA1H 
Find All Approximate Occurrences of a Pattern in a String

701


BA1I 
Find the Most Frequent Words with Mismatches in a String

570


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

509


BA1K 
Generate the Frequency Array of a String

470


BA1L 
Implement PatternToNumber

530


BA1M 
Implement NumberToPattern

494


BA1N 
Generate the dNeighborhood of a String

518


BA2A 
Implement MotifEnumeration

426


BA2B 
Find a Median String

418


BA2C 
Find a Profilemost Probable kmer in a String

444


BA2D 
Implement GreedyMotifSearch

368


BA2E 
Implement GreedyMotifSearch with Pseudocounts

313


BA2F 
Implement RandomizedMotifSearch

251


BA2G 
Implement GibbsSampler

225


BA2H 
Implement DistanceBetweenPatternAndStrings

289


BA3A 
Generate the kmer Composition of a String

542


BA3B 
Reconstruct a String from its Genome Path

478


BA3C 
Construct the Overlap Graph of a Collection of kmers

445


BA3D 
Construct the De Bruijn Graph of a String

442


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

410


BA3F 
Find an Eulerian Cycle in a Graph

304


BA3G 
Find an Eulerian Path in a Graph

252


BA3H 
Reconstruct a String from its kmer Composition

249


BA3I 
Find a kUniversal Circular String

195


BA3J 
Reconstruct a String from its Paired Composition

181


BA3K 
Generate Contigs from a Collection of Reads

176


BA3L 
Construct a String Spelled by a Gapped Genome Path

147


BA3M 
Generate All Maximal NonBranching Paths in a Graph

128


BA4A 
Translate an RNA String into an Amino Acid String

357


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

264


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

264


BA4D 
Compute the Number of Peptides of Given Total Mass

154


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

196


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

158


BA4G 
Implement LeaderboardCyclopeptideSequencing

149


BA4H 
Generate the Convolution of a Spectrum

154


BA4I 
Implement ConvolutionCyclopeptideSequencing

111


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

175


BA4K 
Compute the Score of a Linear Peptide

136


BA4L 
Trim a Peptide Leaderboard

120


BA4M 
Solve the Turnpike Problem

70


BA5A 
Find the Minimum Number of Coins Needed to Make Change

472


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

380


BA5C 
Find a Longest Common Subsequence of Two Strings

472


BA5D 
Find the Longest Path in a DAG

312


BA5E 
Find a HighestScoring Alignment of Two Strings

436


BA5F 
Find a HighestScoring Local Alignment of Two Strings

360


BA5G 
Compute the Edit Distance Between Two Strings

432


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

267


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

243


BA5J 
Align Two Strings Using Affine Gap Penalties

270


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

170


BA5L 
Align Two Strings Using Linear Space

150


BA5M 
Find a HighestScoring Multiple Sequence Alignment

171


BA5N 
Find a Topological Ordering of a DAG

118


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

274


BA6B 
Compute the Number of Breakpoints in a Permutation

299


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

198


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

60


BA6E 
Find All Shared kmers of a Pair of Strings

203


BA6F 
Implement ChromosomeToCycle

120


BA6G 
Implement CycleToChromosome

115


BA6H 
Implement ColoredEdges

105


BA6I 
Implement GraphToGenome

86


BA6J 
Implement 2BreakOnGenomeGraph

80


BA6K 
Implement 2BreakOnGenome

69


BA7A 
Compute Distances Between Leaves

135


BA7B 
Compute Limb Lengths in a Tree

143


BA7C 
Implement AdditivePhylogeny

98


BA7D 
Implement UPGMA

94


BA7E 
Implement the Neighbor Joining Algorithm

80


BA7F 
Implement SmallParsimony

71


BA7G 
Adapt SmallParsimony to Unrooted Trees

46


BA8A 
Implement FarthestFirstTraversal

104


BA8B 
Compute the Squared Error Distortion

98


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

106


BA8D 
Implement the Soft kMeans Clustering Algorithm

87


BA8E 
Implement Hierarchical Clustering

82


BA9A 
Construct a Trie from a Collection of Patterns

237


BA9B 
Implement TrieMatching

210


BA9C 
Construct the Suffix Tree of a String

164


BA9D 
Find the Longest Repeat in a String

191


BA9E 
Find the Longest Substring Shared by Two Strings

180


BA9F 
Find the Shortest NonShared Substring of Two Strings

145


BA9G 
Construct the Suffix Array of a String

189


BA9H 
Pattern Matching with the Suffix Array

103


BA9I 
Construct the BurrowsWheeler Transform of a String

227


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

187


BA9K 
Generate the LasttoFirst Mapping of a String

116


BA9L 
Implement BWMatching

146


BA9M 
Implement BetterBWMatching

132


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

144


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

114


BA9P 
Implement TreeColoring

59


BA9Q 
Construct the Partial Suffix Array of a String

118


BA9R 
Construct a Suffix Tree from a Suffix Array

88

