Korte overzicht, index, lijst die alle paginanummers weergeeft over een bepaald onderwerp om deze snel te vinden in een openboek examen. Specifiek over de slides en cursus van bio-informatica.
Hoofdstuk Onderwerpen Slides Boek pagina's
H1: Intro 7- 28
H2: Background in Database organisation 6 29-30
computer sciences Relational databases 7-8 31
Algorithms 9-14 32-37
Classification problems 33 38
Confusion matrix 35-39 39-42
ROC 40-41 42
Graph theory 43- 58 42-51
Different types of graphs 44--51 42-45
Adjacency matrix 46 46
Adjacency list 47 46
Brute force algorithm 63 51-52
Big-O-notation 65-68 53
Complexity classes 69-72 53-54
Exhaustive vs. heuristic 73 54-55
Search, decision and optimization 74-91 55-59
problems/algorithms
Iterative improvement 82-87 58-59
H3: Pairwise Match/mismatch/hamming distance 7 64-67
alignment Substitution matrix and alignment score 17-22 67-72
o Gap penalties 23-25 72-73
Global vs. local pairwise alignment 32 75
Definitions: similarity/identity/conservation 35-39 77
/Homologs/orthologs/paralogs/xenologs/
analogs
Dot matrix of dotplot 44-50 78-81
o EMBOSS dotplot 50-54 81
Global alignment 55-80 81-93
o Needleman-Wunsch 59-80 84-93
Local alignment 82-91 93-96
o Smith-Waterman
Advanced penalties 92-93 97
Substitution matrices 97-114 98-101
o PAM 115-141 102-106
o Blosum 142-150 106-108
o PAM vs. Blosum 151-154 108
H4: Multiple Use MSA 6-15 111
alignment (MSA) MSA as a graph 20-24
Dynamic methods (exhaustive) 25-37 115-120
o Lipman MSA algorithm 29-30 117-118
o Scoring multiple alignment 31-37 118-120
Progressive methods (heuristic) 39-49 121-125
o Feng-Doolittle algorithm 41-45 121-122
o Clustal W 46-49 122-125
Iterative methods 51-58 125-130
o MAFFT 57 126-127
o MUSLE 53-56 127-128
o SAGA 58 128-130
Consistency-based methods 60-67 130-132
o ProbCons 61 130-131
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