DNAnalyzer/game/level4/slides.html at e968c9587cbec524259e3a80369d3d92748b77fb · StreetScienceCommunity/DNAnalyzer · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
---
layout: slides
title: "Level 4 - Alignment"
---

### Alignment

![Five people hold puzzle pieces of different colors above their heads](images/alignment1.png)

<small><small>[https://www.pinterest.ru/pin/439663982367597812/]</small></small>

???
- Thanks to nanopore sequencing, I receive the unique sequence of DNA.
- But what is next to do with this sequence?
- How to determine the specific organism this DNA belongs to?


---

### Alignment/Mapping

![Five people make an alignment from puzzle pieces of different colors.](images/alignment2.png)

<small><small>[https://marlenechism.com/blog/powerful-forces-intention-alignment/]</small></small>

???
- The answer is to compare this sequence with the so-called reference sequence.
- It is the sequence which serves as a template.

---

### Alignment

![Pairwise alignment of sequence 1 "ACTCG" and sequence 2 "ATTC_". First letters of both sequences are in green frame and marked as "Match". Second letter of both sequences are in red frame and marked as "Mismatch". Last letters of both sequences are in blue frame and marked as "Gap".](images/paiwise-alignment.png)

<small><small>[https://towardsdatascience.com/pairwise-sequence-alignment-using-biopython-d1a9d0ba861f]</small></small>

???
- I can compare sequences by alignment.
- Sequence alignment is an arrangement of two or more sequences, highlighting their similarity.
- Comparing the sequences it could be that one of the sequences has a different nucleotide in one position.
- This is called a Mismatch like the C to T in the red box.
- It could also happen that there is no nucleotide in the second sequence to the one in the first like the G in the blue box. This is called a gap.
- Mismatches in the alignment correspond to mutations, and gaps correspond to insertions or deletions.

---

### Alignment

![Many sequences make up an multiple alignment.](images/multiple-alignment.png)

<small><small>[https://medium.com/@hasini.dbv/pairwise-sequence-alignment-global-and-local-alignments-5ebacf83c752]</small></small>

???
- Alignment is an important instrument for finding a similarity between two or more sequences
- Due to its semi-conservative duplication mechanism, DNA transmits genetic information from generation to generation.
- Changes in the material are sometimes caused by errors or mutations in duplication, or by viruses and other mechanisms that move sequences between individuals and within chromosomes.
- Alignment between sequences indicates that both sequences originated from a common ancestor that contained the matching subsequences.
- In the case of genetic sequences, it implies that their carriers evolved from a common ancestor.

---

### Alignment

https://phylo.cs.mcgill.ca/play.php - learn more about alignment!

???
- Follow this link to play a fun game where you can learn more about alignment.