Bioinformatics Lab CSE470
Book : Bioinformatics Algorithms: an Active Learning Approach
Writers : Phillip Compeau & Pavel Pevzner
Chapter 1
| ID | Title |
|---|---|
| BA1A | Compute the Number of Times a Pattern Appears in a Text |
| BA1B | Find the Most Frequent Words in a String |
| BA1C | Find the Reverse Complement of a String |
| BA1D | Find All Occurrences of a Pattern in a String |
| BA1E | Find Patterns Forming Clumps in a String |
| BA1F | Find a Position in a Genome Minimizing the Skew |
| BA1G | Compute the Hamming Distance Between Two Strings |
| BA1H | Find All Approximate Occurrences of a Pattern in a String |
| BA1I | Find the Most Frequent Words with Mismatches in a String |
| BA1J | Find Frequent Words with Mismatches and Reverse Complements |
| BA1K | Generate the Frequency Array of a String |
| BA1L | Implement PatternToNumber |
| BA1M | Implement NumberToPattern |
| BA1N | Generate the d-Neighborhood of a String |
Chapter 2
| ID | Title |
|---|---|
| BA2A | Implement MotifEnumeration |
| BA2B | Find a Median String |
| BA2C | Find a Profile-most Probable k-mer in a String |
| BA2D | Implement GreedyMotifSearch |
| BA2E | Implement GreedyMotifSearch with Pseudocounts |
| BA2F | Implement RandomizedMotifSearch |
| BA2G | Implement GibbsSampler |
| BA2H | Implement DistanceBetweenPatternAndStrings |
Chapter 3
| ID | Title |
|---|---|
| BA3A | Generate the k-mer Composition of a String |
| BA3B | Reconstruct a String from its Genome Path |
| BA3C | Construct the Overlap Graph of a Collection of k-mers |
| BA3D | Construct the De Bruijn Graph of a String |
| BA3E | Construct the De Bruijn Graph of a Collection of k-mers |
| BA3F | Find an Eulerian Cycle in a Graph |
| BA3G | Find an Eulerian Path in a Graph |
| BA3H | Reconstruct a String from its k-mer Composition |
| BA3I | Find a k-Universal Circular String |
| BA3J | Reconstruct a String from its Paired Composition |
| BA3K | Generate Contigs from a Collection of Reads |
| BA3L | Construct a String Spelled by a Gapped Genome Path |
| BA3M | Generate All Maximal Non-Branching Paths in a Graph |
Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
- Table for chapter 1 2 and 3 was obtained from Sharmin Ahmed
- Lab 5,6 and 4 contains all the codes for
Chapter 4andChapter 9