1 Purpose Flashcards
1 Purpose of Bioinformatic
1.1 Adleman Travelling Sales Problem
1.2 DNA as Information Storage
2 Alignment
2.1 Longest Common Subsequence
2.2 Needleman-Wunsch
2.2.1 Global Alignment Problem
- 3 Smith-Waterman
- 1 Local Alignment Problem
- 3.2 Scoring Gaps
2.4 Affine Gap
2.5 Banded Dynamic Programming
Prefix
Suffix
2.6 Nussinov RNA Folding
3 Trees and Phylogeny
3.1 Distance Matrices to Evolutionary Tree
3.2 Additive Phylogeny
3.3 Least Squares Distance Based Phylogeny
3.4 Ultrametric Evolutionary Trees
3.5 Neighbour Joining
3.6 Character-Based Tree Reconstruction
3.7 Small Parsimony Problem
3.8 Large Parsimony Problem
3.9 Progressive Alignment
4 Genome Sequencing
4.1 Assumptions - largely untrue
4.2 Compute de Bruijn Graph given unknown genome
4.3 Eulerian Graph Problem
4.4 DNA Sequencing with Read-pairs
4.5 Errors
5 Clustering
5.1 Lloyd Algorithm
5.2 Soft Clustering
5.3 Hierarchical Clustering
5.4 Markov Clustering Algorithm
5.5 Stochastic Neighbour Embedding
5.5.1 t-SNE Algorithm
5.6 Burrows Wheeler Transform
6 Genome Assembly and Pattern Matchin
6.1 Genome Compression
7 Hidden Markov Models
- 1 Genomic Sequencing
- 1 Genome Analysis
- 2 HMM Definition
Main Question 1 EVALUATION
Main Question 2 DECODING
Main Question 3 LEARNING
- 3 GeneScan
- 3.1 Features
7.4 Transmembrane HMM
