BA10A 
Compute the Probability of a Hidden Path

451


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

383


BA10C 
Implement the Viterbi Algorithm

241


BA10D 
Compute the Probability of a String Emitted by an HMM

208


BA10E 
Construct a Profile HMM

131


BA10F 
Construct a Profile HMM with Pseudocounts

120


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

64


BA10H 
Estimate the Parameters of an HMM

84


BA10I 
Implement Viterbi Learning

75


BA10J 
Solve the Soft Decoding Problem

78


BA10K 
Implement BaumWelch Learning

61


BA11A 
Construct the Graph of a Spectrum

111


BA11B 
Implement DecodingIdealSpectrum

84


BA11C 
Convert a Peptide into a Peptide Vector

116


BA11D 
Convert a Peptide Vector into a Peptide

110


BA11E 
Sequence a Peptide

67


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

67


BA11G 
Implement PSMSearch

66


BA11H 
Compute the Size of a Spectral Dictionary

55


BA11I 
Compute the Probability of a Spectral Dictionary

55


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

44


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

993


BA1B 
Find the Most Frequent Words in a String

1159


BA1C 
Find the Reverse Complement of a String

1118


BA1D 
Find All Occurrences of a Pattern in a String

1015


BA1E 
Find Patterns Forming Clumps in a String

800


BA1F 
Find a Position in a Genome Minimizing the Skew

775


BA1G 
Compute the Hamming Distance Between Two Strings

855


BA1H 
Find All Approximate Occurrences of a Pattern in a String

735


BA1I 
Find the Most Frequent Words with Mismatches in a String

596


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

538


BA1K 
Generate the Frequency Array of a String

495


BA1L 
Implement PatternToNumber

550


BA1M 
Implement NumberToPattern

515


BA1N 
Generate the dNeighborhood of a String

541


BA2A 
Implement MotifEnumeration

443


BA2B 
Find a Median String

441


BA2C 
Find a Profilemost Probable kmer in a String

464


BA2D 
Implement GreedyMotifSearch

386


BA2E 
Implement GreedyMotifSearch with Pseudocounts

333


BA2F 
Implement RandomizedMotifSearch

266


BA2G 
Implement GibbsSampler

242


BA2H 
Implement DistanceBetweenPatternAndStrings

307


BA3A 
Generate the kmer Composition of a String

571


BA3B 
Reconstruct a String from its Genome Path

504


BA3C 
Construct the Overlap Graph of a Collection of kmers

474


BA3D 
Construct the De Bruijn Graph of a String

475


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

431


BA3F 
Find an Eulerian Cycle in a Graph

327


BA3G 
Find an Eulerian Path in a Graph

270


BA3H 
Reconstruct a String from its kmer Composition

272


BA3I 
Find a kUniversal Circular String

214


BA3J 
Reconstruct a String from its Paired Composition

191


BA3K 
Generate Contigs from a Collection of Reads

192


BA3L 
Construct a String Spelled by a Gapped Genome Path

159


BA3M 
Generate All Maximal NonBranching Paths in a Graph

141


BA4A 
Translate an RNA String into an Amino Acid String

374


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

287


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

277


BA4D 
Compute the Number of Peptides of Given Total Mass

172


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

208


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

168


BA4G 
Implement LeaderboardCyclopeptideSequencing

159


BA4H 
Generate the Convolution of a Spectrum

160


BA4I 
Implement ConvolutionCyclopeptideSequencing

118


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

182


BA4K 
Compute the Score of a Linear Peptide

141


BA4L 
Trim a Peptide Leaderboard

126


BA4M 
Solve the Turnpike Problem

73


BA5A 
Find the Minimum Number of Coins Needed to Make Change

485


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

394


BA5C 
Find a Longest Common Subsequence of Two Strings

485


BA5D 
Find the Longest Path in a DAG

322


BA5E 
Find a HighestScoring Alignment of Two Strings

456


BA5F 
Find a HighestScoring Local Alignment of Two Strings

372


BA5G 
Compute the Edit Distance Between Two Strings

442


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

271


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

248


BA5J 
Align Two Strings Using Affine Gap Penalties

277


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

178


BA5L 
Align Two Strings Using Linear Space

159


BA5M 
Find a HighestScoring Multiple Sequence Alignment

179


BA5N 
Find a Topological Ordering of a DAG

123


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

285


BA6B 
Compute the Number of Breakpoints in a Permutation

313


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

206


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

64


BA6E 
Find All Shared kmers of a Pair of Strings

209


BA6F 
Implement ChromosomeToCycle

124


BA6G 
Implement CycleToChromosome

120


BA6H 
Implement ColoredEdges

110


BA6I 
Implement GraphToGenome

90


BA6J 
Implement 2BreakOnGenomeGraph

84


BA6K 
Implement 2BreakOnGenome

76


BA7A 
Compute Distances Between Leaves

140


BA7B 
Compute Limb Lengths in a Tree

151


BA7C 
Implement AdditivePhylogeny

106


BA7D 
Implement UPGMA

104


BA7E 
Implement the Neighbor Joining Algorithm

86


BA7F 
Implement SmallParsimony

79


BA7G 
Adapt SmallParsimony to Unrooted Trees

48


BA8A 
Implement FarthestFirstTraversal

110


BA8B 
Compute the Squared Error Distortion

105


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

116


BA8D 
Implement the Soft kMeans Clustering Algorithm

94


BA8E 
Implement Hierarchical Clustering

90


BA9A 
Construct a Trie from a Collection of Patterns

243


BA9B 
Implement TrieMatching

217


BA9C 
Construct the Suffix Tree of a String

168


BA9D 
Find the Longest Repeat in a String

197


BA9E 
Find the Longest Substring Shared by Two Strings

183


BA9F 
Find the Shortest NonShared Substring of Two Strings

148


BA9G 
Construct the Suffix Array of a String

200


BA9H 
Pattern Matching with the Suffix Array

110


BA9I 
Construct the BurrowsWheeler Transform of a String

240


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

197


BA9K 
Generate the LasttoFirst Mapping of a String

125


BA9L 
Implement BWMatching

155


BA9M 
Implement BetterBWMatching

140


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

152


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

119


BA9P 
Implement TreeColoring

60


BA9Q 
Construct the Partial Suffix Array of a String

120


BA9R 
Construct a Suffix Tree from a Suffix Array

91

