BA10A 
Compute the Probability of a Hidden Path

236


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

197


BA10C 
Implement the Viterbi Algorithm

122


BA10D 
Compute the Probability of a String Emitted by an HMM

109


BA10E 
Construct a Profile HMM

80


BA10F 
Construct a Profile HMM with Pseudocounts

70


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

31


BA10H 
Estimate the Parameters of an HMM

41


BA10I 
Implement Viterbi Learning

35


BA10J 
Solve the Soft Decoding Problem

32


BA10K 
Implement BaumWelch Learning

24


BA11A 
Construct the Graph of a Spectrum

64


BA11B 
Implement DecodingIdealSpectrum

48


BA11C 
Convert a Peptide into a Peptide Vector

69


BA11D 
Convert a Peptide Vector into a Peptide

63


BA11E 
Sequence a Peptide

41


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

42


BA11G 
Implement PSMSearch

39


BA11H 
Compute the Size of a Spectral Dictionary

35


BA11I 
Compute the Probability of a Spectral Dictionary

34


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

26


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

450


BA1B 
Find the Most Frequent Words in a String

624


BA1C 
Find the Reverse Complement of a String

563


BA1D 
Find All Occurrences of a Pattern in a String

532


BA1E 
Find Patterns Forming Clumps in a String

434


BA1F 
Find a Position in a Genome Minimizing the Skew

408


BA1G 
Compute the Hamming Distance Between Two Strings

375


BA1H 
Find All Approximate Occurrences of a Pattern in a String

418


BA1I 
Find the Most Frequent Words with Mismatches in a String

325


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

297


BA1K 
Generate the Frequency Array of a String

270


BA1L 
Implement PatternToNumber

281


BA1M 
Implement NumberToPattern

270


BA1N 
Generate the dNeighborhood of a String

299


BA2A 
Implement MotifEnumeration

258


BA2B 
Find a Median String

218


BA2C 
Find a Profilemost Probable kmer in a String

237


BA2D 
Implement GreedyMotifSearch

191


BA2E 
Implement GreedyMotifSearch with Pseudocounts

159


BA2F 
Implement RandomizedMotifSearch

133


BA2G 
Implement GibbsSampler

122


BA2H 
Implement DistanceBetweenPatternAndStrings

157


BA3A 
Generate the kmer Composition of a String

258


BA3B 
Reconstruct a String from its Genome Path

211


BA3C 
Construct the Overlap Graph of a Collection of kmers

215


BA3D 
Construct the De Bruijn Graph of a String

204


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

186


BA3F 
Find an Eulerian Cycle in a Graph

140


BA3G 
Find an Eulerian Path in a Graph

126


BA3H 
Reconstruct a String from its kmer Composition

129


BA3I 
Find a kUniversal Circular String

106


BA3J 
Reconstruct a String from its Paired Composition

84


BA3K 
Generate Contigs from a Collection of Reads

95


BA3L 
Construct a String Spelled by a Gapped Genome Path

81


BA3M 
Generate All Maximal NonBranching Paths in a Graph

83


BA4A 
Translate an RNA String into an Amino Acid String

189


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

153


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

152


BA4D 
Compute the Number of Peptides of Given Total Mass

73


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

104


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

92


BA4G 
Implement LeaderboardCyclopeptideSequencing

87


BA4H 
Generate the Convolution of a Spectrum

89


BA4I 
Implement ConvolutionCyclopeptideSequencing

60


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

95


BA4K 
Compute the Score of a Linear Peptide

78


BA4L 
Trim a Peptide Leaderboard

66


BA4M 
Solve the Turnpike Problem

39


BA5A 
Find the Minimum Number of Coins Needed to Make Change

354


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

296


BA5C 
Find a Longest Common Subsequence of Two Strings

344


BA5D 
Find the Longest Path in a DAG

244


BA5E 
Find a HighestScoring Alignment of Two Strings

263


BA5F 
Find a HighestScoring Local Alignment of Two Strings

229


BA5G 
Compute the Edit Distance Between Two Strings

285


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

181


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

173


BA5J 
Align Two Strings Using Affine Gap Penalties

159


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

118


BA5L 
Align Two Strings Using Linear Space

100


BA5M 
Find a HighestScoring Multiple Sequence Alignment

123


BA5N 
Find a Topological Ordering of a DAG

70


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

220


BA6B 
Compute the Number of Breakpoints in a Permutation

235


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

155


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

32


BA6E 
Find All Shared kmers of a Pair of Strings

163


BA6F 
Implement ChromosomeToCycle

78


BA6G 
Implement CycleToChromosome

73


BA6H 
Implement ColoredEdges

69


BA6I 
Implement GraphToGenome

54


BA6J 
Implement 2BreakOnGenomeGraph

52


BA6K 
Implement 2BreakOnGenome

38


BA7A 
Compute Distances Between Leaves

94


BA7B 
Compute Limb Lengths in a Tree

88


BA7C 
Implement AdditivePhylogeny

59


BA7D 
Implement UPGMA

53


BA7E 
Implement the Neighbor Joining Algorithm

47


BA7F 
Implement SmallParsimony

40


BA7G 
Adapt SmallParsimony to Unrooted Trees

26


BA8A 
Implement FarthestFirstTraversal

62


BA8B 
Compute the Squared Error Distortion

60


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

59


BA8D 
Implement the Soft kMeans Clustering Algorithm

56


BA8E 
Implement Hierarchical Clustering

47


BA9A 
Construct a Trie from a Collection of Patterns

187


BA9B 
Implement TrieMatching

164


BA9C 
Construct the Suffix Tree of a String

127


BA9D 
Find the Longest Repeat in a String

142


BA9E 
Find the Longest Substring Shared by Two Strings

137


BA9F 
Find the Shortest NonShared Substring of Two Strings

107


BA9G 
Construct the Suffix Array of a String

143


BA9H 
Pattern Matching with the Suffix Array

65


BA9I 
Construct the BurrowsWheeler Transform of a String

166


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

138


BA9K 
Generate the LasttoFirst Mapping of a String

60


BA9L 
Implement BWMatching

105


BA9M 
Implement BetterBWMatching

100


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

113


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

86


BA9P 
Implement TreeColoring

36


BA9Q 
Construct the Partial Suffix Array of a String

87


BA9R 
Construct a Suffix Tree from a Suffix Array

63

