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Aantekeningen hoorcollege 3: Alignments . Introduction to Bioinformatics $4.83
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Aantekeningen hoorcollege 3: Alignments . Introduction to Bioinformatics
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  • Course
  • Introduction to Bioinformatics
  • Institution
  • Vrije Universiteit Amsterdam (VU)

The notes from lecture 3 on Alignments in the course introduction to bioinformatics. The document contains clear images. Furthermore, it is organized and clearly marked.

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Document information

  • February 14, 2024
  • 6
  • 2023/2024
  • Class notes
  • Evert bosdriesz
  • Hoorcollege 3

Subjects

  • alignments
  • bioinformatics
  • mutations
  • snp
  • snv
  • homology
  • conserved regions
  • substitution matrix
  • psi blast
  • blast
  • pssm
  • sequence alignment algorithms

Written for

  • Vrije Universiteit Amsterdam (VU)
  • Medische Natuurwetenschappen
  • Introduction to Bioinformatics
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Introduction to bioinformatics
Hoorcollege 3 – 15 januari 2024
Alignments
Introduction: DNA, proteins and mutations
DNA is a macromolecule. Big molecule with small units
Bases: Adenine, Guanine, Thymine, Cytosine


FASTA format
Each sequence begins with the symbol “>”
First line is the sequence description and following lines until next header are the protein (or
nucleotide) sequence


Central dogma of molecular biology
From DNA to RNA to proteins
Transcription and translation
RNA divides in codons


The codon table
Which combination of nucleotides are which amino acid
Stopcodon: translation stops


Mutation: change in DNA sequence
Reference genome (GRCh38)
- 3x109 base pairs
- 20 000 proteins coding genes
- 1,5% coding
- 3.7x1013 cells
Point mutation: one base is changed
SNV = single nucleotide variant
- A position in the DNA where a person/cell has a different nucleotide than the
reference genome
SNP = single nucleotide polymorphism
- A position in the DNA where a change is present in at least 1% of the population

, Types of mutations
Nt change :
- Transition A  G or T  C
o Niet dezelfde groep
- Transversion A/G  T/C oftwel A  T or G  C
o Dezelfde groep

Aa change:
- Synonymous TTC  TTT
o does not result in a change to the amino acid sequence of the
protein
- Nonsynonymous
o result in a change to the amino acid sequence of the protein
o Nonsense TTC  ATC
 Ontstaat een stopcodon
o Missense
 A substitution that results in a change in the amino acid
sequence of a protein
 Conservative TTC  TCC
 amino acid is replaced by a different amino acid with
similar chemical properties
 Non conservative TTC  TGC
 Substitution has different properties
Al of this is a point mutation, only one base changes
Insertion and deletion cause frameshifts
Alle opvolgende condons zijn hierdoor veranderd


Quiz: which change a frameshift?
Deletion of 2 nucleotides: yes  rest changes
Insertion of 3 nucleotides: no  only when it’s a stopcodon, but that is not a frameshift
Insertion of 4 nucleotides: yes  rest changes


Evolution, phylogeny and alignments
Mutations are random
Most mutations are nearly neutral  genetic drift as driver of molecular evolution
Genetic diversity together with selection are the driving forces of adaptative evolution
Phylogenetic tree: branching diagram that describes evolutionary relationships

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