BA10A 
Compute the Probability of a Hidden Path

414


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

352


BA10C 
Implement the Viterbi Algorithm

214


BA10D 
Compute the Probability of a String Emitted by an HMM

187


BA10E 
Construct a Profile HMM

120


BA10F 
Construct a Profile HMM with Pseudocounts

111


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

56


BA10H 
Estimate the Parameters of an HMM

73


BA10I 
Implement Viterbi Learning

65


BA10J 
Solve the Soft Decoding Problem

64


BA10K 
Implement BaumWelch Learning

52


BA11A 
Construct the Graph of a Spectrum

99


BA11B 
Implement DecodingIdealSpectrum

71


BA11C 
Convert a Peptide into a Peptide Vector

104


BA11D 
Convert a Peptide Vector into a Peptide

98


BA11E 
Sequence a Peptide

58


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

59


BA11G 
Implement PSMSearch

58


BA11H 
Compute the Size of a Spectral Dictionary

49


BA11I 
Compute the Probability of a Spectral Dictionary

49


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

38


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

880


BA1B 
Find the Most Frequent Words in a String

1048


BA1C 
Find the Reverse Complement of a String

996


BA1D 
Find All Occurrences of a Pattern in a String

909


BA1E 
Find Patterns Forming Clumps in a String

697


BA1F 
Find a Position in a Genome Minimizing the Skew

687


BA1G 
Compute the Hamming Distance Between Two Strings

760


BA1H 
Find All Approximate Occurrences of a Pattern in a String

656


BA1I 
Find the Most Frequent Words with Mismatches in a String

524


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

469


BA1K 
Generate the Frequency Array of a String

439


BA1L 
Implement PatternToNumber

494


BA1M 
Implement NumberToPattern

455


BA1N 
Generate the dNeighborhood of a String

479


BA2A 
Implement MotifEnumeration

393


BA2B 
Find a Median String

385


BA2C 
Find a Profilemost Probable kmer in a String

404


BA2D 
Implement GreedyMotifSearch

333


BA2E 
Implement GreedyMotifSearch with Pseudocounts

283


BA2F 
Implement RandomizedMotifSearch

230


BA2G 
Implement GibbsSampler

208


BA2H 
Implement DistanceBetweenPatternAndStrings

263


BA3A 
Generate the kmer Composition of a String

488


BA3B 
Reconstruct a String from its Genome Path

449


BA3C 
Construct the Overlap Graph of a Collection of kmers

394


BA3D 
Construct the De Bruijn Graph of a String

407


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

383


BA3F 
Find an Eulerian Cycle in a Graph

281


BA3G 
Find an Eulerian Path in a Graph

236


BA3H 
Reconstruct a String from its kmer Composition

228


BA3I 
Find a kUniversal Circular String

171


BA3J 
Reconstruct a String from its Paired Composition

163


BA3K 
Generate Contigs from a Collection of Reads

167


BA3L 
Construct a String Spelled by a Gapped Genome Path

138


BA3M 
Generate All Maximal NonBranching Paths in a Graph

115


BA4A 
Translate an RNA String into an Amino Acid String

341


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

249


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

245


BA4D 
Compute the Number of Peptides of Given Total Mass

133


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

171


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

141


BA4G 
Implement LeaderboardCyclopeptideSequencing

132


BA4H 
Generate the Convolution of a Spectrum

132


BA4I 
Implement ConvolutionCyclopeptideSequencing

99


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

151


BA4K 
Compute the Score of a Linear Peptide

116


BA4L 
Trim a Peptide Leaderboard

100


BA4M 
Solve the Turnpike Problem

68


BA5A 
Find the Minimum Number of Coins Needed to Make Change

455


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

366


BA5C 
Find a Longest Common Subsequence of Two Strings

450


BA5D 
Find the Longest Path in a DAG

300


BA5E 
Find a HighestScoring Alignment of Two Strings

404


BA5F 
Find a HighestScoring Local Alignment of Two Strings

332


BA5G 
Compute the Edit Distance Between Two Strings

406


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

253


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

232


BA5J 
Align Two Strings Using Affine Gap Penalties

249


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

164


BA5L 
Align Two Strings Using Linear Space

144


BA5M 
Find a HighestScoring Multiple Sequence Alignment

167


BA5N 
Find a Topological Ordering of a DAG

108


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

267


BA6B 
Compute the Number of Breakpoints in a Permutation

291


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

191


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

55


BA6E 
Find All Shared kmers of a Pair of Strings

197


BA6F 
Implement ChromosomeToCycle

114


BA6G 
Implement CycleToChromosome

109


BA6H 
Implement ColoredEdges

99


BA6I 
Implement GraphToGenome

81


BA6J 
Implement 2BreakOnGenomeGraph

74


BA6K 
Implement 2BreakOnGenome

64


BA7A 
Compute Distances Between Leaves

128


BA7B 
Compute Limb Lengths in a Tree

137


BA7C 
Implement AdditivePhylogeny

92


BA7D 
Implement UPGMA

88


BA7E 
Implement the Neighbor Joining Algorithm

75


BA7F 
Implement SmallParsimony

67


BA7G 
Adapt SmallParsimony to Unrooted Trees

43


BA8A 
Implement FarthestFirstTraversal

98


BA8B 
Compute the Squared Error Distortion

94


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

100


BA8D 
Implement the Soft kMeans Clustering Algorithm

81


BA8E 
Implement Hierarchical Clustering

77


BA9A 
Construct a Trie from a Collection of Patterns

229


BA9B 
Implement TrieMatching

202


BA9C 
Construct the Suffix Tree of a String

159


BA9D 
Find the Longest Repeat in a String

185


BA9E 
Find the Longest Substring Shared by Two Strings

175


BA9F 
Find the Shortest NonShared Substring of Two Strings

140


BA9G 
Construct the Suffix Array of a String

185


BA9H 
Pattern Matching with the Suffix Array

99


BA9I 
Construct the BurrowsWheeler Transform of a String

217


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

179


BA9K 
Generate the LasttoFirst Mapping of a String

108


BA9L 
Implement BWMatching

139


BA9M 
Implement BetterBWMatching

126


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

140


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

111


BA9P 
Implement TreeColoring

54


BA9Q 
Construct the Partial Suffix Array of a String

113


BA9R 
Construct a Suffix Tree from a Suffix Array

84

