1 Purpose Flashcards

(42 cards)

1
Q

1 Purpose of Bioinformatic

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2
Q

1.1 Adleman Travelling Sales Problem

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3
Q

1.2 DNA as Information Storage

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4
Q

2 Alignment

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5
Q

2.1 Longest Common Subsequence

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6
Q

2.2 Needleman-Wunsch

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7
Q

2.2.1 Global Alignment Problem

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8
Q
  1. 3 Smith-Waterman
    1. 1 Local Alignment Problem
  2. 3.2 Scoring Gaps
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9
Q

2.4 Affine Gap

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10
Q

2.5 Banded Dynamic Programming

Prefix

Suffix

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11
Q

2.6 Nussinov RNA Folding

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12
Q

3 Trees and Phylogeny

3.1 Distance Matrices to Evolutionary Tree

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13
Q

3.2 Additive Phylogeny

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14
Q

3.3 Least Squares Distance Based Phylogeny

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15
Q

3.4 Ultrametric Evolutionary Trees

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16
Q

3.5 Neighbour Joining

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17
Q

3.6 Character-Based Tree Reconstruction

18
Q

3.7 Small Parsimony Problem

19
Q

3.8 Large Parsimony Problem

20
Q

3.9 Progressive Alignment

21
Q

4 Genome Sequencing

4.1 Assumptions - largely untrue

22
Q

4.2 Compute de Bruijn Graph given unknown genome

23
Q

4.3 Eulerian Graph Problem

24
Q

4.4 DNA Sequencing with Read-pairs

25
4.5 Errors
26
5 Clustering
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5.1 Lloyd Algorithm
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5.2 Soft Clustering
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5.3 Hierarchical Clustering
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5.4 Markov Clustering Algorithm
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5.5 Stochastic Neighbour Embedding
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5.5.1 t-SNE Algorithm
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5.6 Burrows Wheeler Transform
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6 Genome Assembly and Pattern Matchin
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6.1 Genome Compression
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7 Hidden Markov Models 7. 1 Genomic Sequencing 7. 1. 1 Genome Analysis
37
7. 2 HMM Definition
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Main Question 1 EVALUATION
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Main Question 2 DECODING
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Main Question 3 LEARNING
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7. 3 GeneScan 7. 3.1 Features
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7.4 Transmembrane HMM