Introduction to Bioinformatics
2023-2024
Nguyen Thuy Vy
Vo Tri Nam
Hong Vu Thuy Uyen
Introduction to Bioinformatics 1
COURSE GOALS/LEARNING OUTOMES
LO General description
G1 Understand the increasing necessity for bioinformatics in modern life sciences research
G2 Describe the central role and major scopes of biological databases
Describe common bioinformatics algorithms in sequence comparisons and sequence-
G3
based database searches
G4 Present some bioinformatics tools applied in drug design based on protein structure
Understand genomics approaches including – genome sequencing, comparative and
G5
functional genomics
G6 Apply presented bioinformatics approaches to address biological questions
Introduction to Bioinformatics 2
CLASS SYLLABUS
Week Topic LO Instructor
Introduction
1 G1 NGUYEN Thuy Vy
Biological foundations of bioinformatics
2 Biological databases G2, G6 VO Tri Nam
Sequence comparisons and sequence-based database
3 G3, G6 VO Tri Nam
searches
Protein structures and structure-based rational drug
4 G4, G6 VO Tri Nam
design
5 Genomics - Genome sequencing G5, G6 NGUYEN Thuy Vy
Genome annotation
6 G5, G6 NGUYEN Thuy Vy
Comparative genome analyses
Introduction to Bioinformatics 3
Genomics
4
The Genome
5
6
Genomes vary in size and content
7
8
Gene structure
9
Why we care about sequencing and
analyzing the genome?
10
Why we care about sequencing the genome?
Môi trường, epigenetics
Central Dogma
Phenotype
11
Genomics: tool for basic science
12
GIẢI MÃ
XÁC ĐỊNH CƠ CHẾ
GÂY BỆNH
CHẨN ĐOÁN
PHÂN TỬ & LIỆU
Bộ gene người
PHÁP GENE
Bộ gene các sinh
vật khác
13
Genomics: tool for medicine
14
Genomes, Transcriptomes, and Proteomes
Central Dogma
Bioinformatics
15
Genomics: shaped by technology
16
The sequencing cost
17
Sequencing technologies and
NGS overview
18
What is DNA sequencing?
19
Whole genome sequencing (WGS) method
A clone-by-
clone, or map-
based,
approach
20
WGS method
Whole-genome
shotgun, the
most common
approach
21
WGS methods
A clone-by-clone, or map-based,
Shotgun approach approach
22
Sequencing technologies
23
Polymerase chain reaction (PCR)
24
Sanger sequencing
25
26
NGS overview
27
NGS overview
28
29
30
NGS
technologies
Sequencing by
synthesis (Illumina)
31
NGS
technologies
Sequencing by
synthesis (Illumina)
32
33
Định dạng file dữ liệu thô fastq
34
NGS
technologies
Ion torrent
(Thermo)
35
Two major approaches for genome sequencing data
36
Genome assembly (de novo assembly)
37
De novo assembly
OLC: Overlap
Layer Consensus
38
De novo assembly
Input
39
De novo assembly
40
De novo assembly
41
Resequencing for variant detection
42
Resequencing for variant detection
Variant selection criteria: coverage > …X
43
Dealing with repeat regions
44
Next NGS (long-read)
45
Next NGS (long-read)
46
PacBio and ONT can use unaltered DNA to detect methylation
https://en.wikipedia.org/wiki/Third-generation_sequencing#/media/File:3rd_gen_Epigenetics.png
47
Portable sequencing
devices
Third generation
sequencing
48
NGS technologies
Data analysis
49
