Tasks: 1 – 5
Rosalind problems
- Find Patterns Forming Clumps in a String
- Find a Position in a Genome Minimizing the Skew
- Find All Approximate Occurrences of a Pattern in a String
- Find the Most Frequent Words with Mismatches in a String
- Find Frequent Words with Mismatches and Reverse Complements
Tasks: 6 – 10
Rosalind problems
- Implement GreedyMotifSearch
- Implement GreedyMotifSearch with Pseudocounts
- Implement RandomizedMotifSearch
- Implement GibbsSampler
- Implement DistanceBetweenPatternAndStrings
Tasks: 11 – 15
Rosalind problems
- Reconstruct a String from its k-mer Composition
- Find a k-Universal Circular String
- Reconstruct a String from its Paired Composition
- Generate Contigs from a Collection of Reads
- Construct a String Spelled by a Gapped Genome Path
Tasks: 16 – 20
Rosalind problems
- Find Substrings of a Genome Encoding a Given Amino Acid String
- Compute the Number of Peptides of Given Total Mass
- Find a Cyclic Peptide with Theoretical Spectrum Matching an Ideal Spectrum
- Implement LeaderboardCyclopeptideSequencing
- Implement ConvolutionCyclopeptideSequencing
Tasks: 21 – 25
Rosalind problems
- Find the Minimum Number of Coins Needed to Make Change
- Find the Length of a Longest Path in a Manhattan-like Grid
- Find a Highest-Scoring Alignment of Two Strings
- Find a Highest-Scoring Local Alignment of Two Strings
- Find a Highest-Scoring Multiple Sequence Alignment
Tasks: 26 – 30
Rosalind problems
- Implement GreedySorting to Sort a Permutation by Reversals
- Compute the Number of Breakpoints in a Permutation
- Compute the 2-Break Distance Between a Pair of Genomes
- Find a Shortest Transformation of One Genome into Another by 2-Breaks
- Implement 2-BreakOnGenome
Additional info here (in this chapter) usefull for 2 last problems:
