BA10A 
Compute the Probability of a Hidden Path

533


BA10B 
Compute the Probability of an Outcome Given a Hidden Path

448


BA10C 
Implement the Viterbi Algorithm

268


BA10D 
Compute the Probability of a String Emitted by an HMM

229


BA10E 
Construct a Profile HMM

141


BA10F 
Construct a Profile HMM with Pseudocounts

131


BA10G 
Perform a Multiple Sequence Alignment with a Profile HMM

74


BA10H 
Estimate the Parameters of an HMM

100


BA10I 
Implement Viterbi Learning

85


BA10J 
Solve the Soft Decoding Problem

92


BA10K 
Implement BaumWelch Learning

73


BA11A 
Construct the Graph of a Spectrum

126


BA11B 
Implement DecodingIdealSpectrum

94


BA11C 
Convert a Peptide into a Peptide Vector

130


BA11D 
Convert a Peptide Vector into a Peptide

125


BA11E 
Sequence a Peptide

75


BA11F 
Find a HighestScoring Peptide in a Proteome against a Spectrum

74


BA11G 
Implement PSMSearch

72


BA11H 
Compute the Size of a Spectral Dictionary

64


BA11I 
Compute the Probability of a Spectral Dictionary

63


BA11J 
Find a HighestScoring Modified Peptide against a Spectrum

47


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

1330


BA1B 
Find the Most Frequent Words in a String

1496


BA1C 
Find the Reverse Complement of a String

1449


BA1D 
Find All Occurrences of a Pattern in a String

1341


BA1E 
Find Patterns Forming Clumps in a String

1060


BA1F 
Find a Position in a Genome Minimizing the Skew

1072


BA1G 
Compute the Hamming Distance Between Two Strings

1127


BA1H 
Find All Approximate Occurrences of a Pattern in a String

937


BA1I 
Find the Most Frequent Words with Mismatches in a String

766


BA1J 
Find Frequent Words with Mismatches and Reverse Complements

701


BA1K 
Generate the Frequency Array of a String

649


BA1L 
Implement PatternToNumber

703


BA1M 
Implement NumberToPattern

669


BA1N 
Generate the dNeighborhood of a String

680


BA2A 
Implement MotifEnumeration

566


BA2B 
Find a Median String

573


BA2C 
Find a Profilemost Probable kmer in a String

582


BA2D 
Implement GreedyMotifSearch

487


BA2E 
Implement GreedyMotifSearch with Pseudocounts

425


BA2F 
Implement RandomizedMotifSearch

348


BA2G 
Implement GibbsSampler

300


BA2H 
Implement DistanceBetweenPatternAndStrings

390


BA3A 
Generate the kmer Composition of a String

701


BA3B 
Reconstruct a String from its Genome Path

626


BA3C 
Construct the Overlap Graph of a Collection of kmers

586


BA3D 
Construct the De Bruijn Graph of a String

612


BA3E 
Construct the De Bruijn Graph of a Collection of kmers

539


BA3F 
Find an Eulerian Cycle in a Graph

409


BA3G 
Find an Eulerian Path in a Graph

347


BA3H 
Reconstruct a String from its kmer Composition

370


BA3I 
Find a kUniversal Circular String

272


BA3J 
Reconstruct a String from its Paired Composition

234


BA3K 
Generate Contigs from a Collection of Reads

236


BA3L 
Construct a String Spelled by a Gapped Genome Path

196


BA3M 
Generate All Maximal NonBranching Paths in a Graph

184


BA4A 
Translate an RNA String into an Amino Acid String

462


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

372


BA4C 
Generate the Theoretical Spectrum of a Cyclic Peptide

358


BA4D 
Compute the Number of Peptides of Given Total Mass

235


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

267


BA4F 
Compute the Score of a Cyclic Peptide Against a Spectrum

218


BA4G 
Implement LeaderboardCyclopeptideSequencing

204


BA4H 
Generate the Convolution of a Spectrum

208


BA4I 
Implement ConvolutionCyclopeptideSequencing

145


BA4J 
Generate the Theoretical Spectrum of a Linear Peptide

227


BA4K 
Compute the Score of a Linear Peptide

178


BA4L 
Trim a Peptide Leaderboard

159


BA4M 
Solve the Turnpike Problem

87


BA5A 
Find the Minimum Number of Coins Needed to Make Change

555


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

445


BA5C 
Find a Longest Common Subsequence of Two Strings

553


BA5D 
Find the Longest Path in a DAG

358


BA5E 
Find a HighestScoring Alignment of Two Strings

530


BA5F 
Find a HighestScoring Local Alignment of Two Strings

420


BA5G 
Compute the Edit Distance Between Two Strings

479


BA5H 
Find a HighestScoring Fitting Alignment of Two Strings

305


BA5I 
Find a HighestScoring Overlap Alignment of Two Strings

271


BA5J 
Align Two Strings Using Affine Gap Penalties

314


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

195


BA5L 
Align Two Strings Using Linear Space

174


BA5M 
Find a HighestScoring Multiple Sequence Alignment

206


BA5N 
Find a Topological Ordering of a DAG

143


BA6A 
Implement GreedySorting to Sort a Permutation by Reversals

324


BA6B 
Compute the Number of Breakpoints in a Permutation

357


BA6C 
Compute the 2Break Distance Between a Pair of Genomes

238


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

83


BA6E 
Find All Shared kmers of a Pair of Strings

219


BA6F 
Implement ChromosomeToCycle

139


BA6G 
Implement CycleToChromosome

134


BA6H 
Implement ColoredEdges

122


BA6I 
Implement GraphToGenome

100


BA6J 
Implement 2BreakOnGenomeGraph

98


BA6K 
Implement 2BreakOnGenome

94


BA7A 
Compute Distances Between Leaves

183


BA7B 
Compute Limb Lengths in a Tree

190


BA7C 
Implement AdditivePhylogeny

153


BA7D 
Implement UPGMA

141


BA7E 
Implement the Neighbor Joining Algorithm

118


BA7F 
Implement SmallParsimony

94


BA7G 
Adapt SmallParsimony to Unrooted Trees

63


BA8A 
Implement FarthestFirstTraversal

129


BA8B 
Compute the Squared Error Distortion

122


BA8C 
Implement the Lloyd Algorithm for kMeans Clustering

135


BA8D 
Implement the Soft kMeans Clustering Algorithm

103


BA8E 
Implement Hierarchical Clustering

101


BA9A 
Construct a Trie from a Collection of Patterns

272


BA9B 
Implement TrieMatching

244


BA9C 
Construct the Suffix Tree of a String

184


BA9D 
Find the Longest Repeat in a String

214


BA9E 
Find the Longest Substring Shared by Two Strings

195


BA9F 
Find the Shortest NonShared Substring of Two Strings

162


BA9G 
Construct the Suffix Array of a String

233


BA9H 
Pattern Matching with the Suffix Array

130


BA9I 
Construct the BurrowsWheeler Transform of a String

279


BA9J 
Reconstruct a String from its BurrowsWheeler Transform

223


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

