[PPT] - Review Session I CS 466 Wesley Wei Qian March 10th 2020 Midterm PowerPoint Presentation

SLIDE 1

Review Session I

CS 466

Wesley Wei Qian March 10th 2020

SLIDE 2

Midterm Exam

This Thursday!

○ 03/12 class time

Different building!

○ Nature History Building Room 2079

Topics

SLIDE 3

Topics we have covered:

Molecular Biology
Probability and Statistics
Sequence and Alignment
Pattern Matching
BLAST

SLIDE 4

Molecular Biology

Molecules
DNA
RNA
Protein (polypeptide)
Molecular Process
Transcription
Translation
Protein folding
Gene splicing: intron/exon
Gene regulation
Genome

SLIDE 5

Probability and Statistics

SLIDE 6

Probability and Statistics

SLIDE 7

Probability and Statistics

SLIDE 8

Probability and Statistics

SLIDE 9

Probability and Statistics

SLIDE 10

Probability and Statistics

SLIDE 11

Probability and Statistics

SLIDE 12

Sequence and Alignment

SLIDE 13

Sequence and Alignment

Global Alignment Local Alignment

SLIDE 14

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 15

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 16

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 17

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 18

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

DDOGC D-OG-

SLIDE 19

Sequence and Alignment

* D D O G C *

2
4
6
8
10

D

2

1

1
3
5
7

O

4
1
2
4

G

6
3
2
1

1

1

Global Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

DDOGC

DOG-

SLIDE 20

Sequence and Alignment

* D D O G C * D 1 1 O 2 G 3 1

Local Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 21

Sequence and Alignment

* D D O G C * D 1 1 O 2 G 3 1

Local Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 22

Sequence and Alignment

* D D O G C * D 1 1 O 2 G 3 1

Local Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 23

Sequence and Alignment

* D D O G C * D 1 1 O 2 G 3 1

Local Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

SLIDE 24

Sequence and Alignment

* D D O G C * D 1 1 O 2 G 3

Local Alignment: DDOGC vs DOG

+1 Match; -1 Mismatch; -2 Gap.

DOG-

DOG

SLIDE 25

Sequence and Alignment Complexity?

SLIDE 26

Sequence and Alignment Complexity?

SLIDE 27

Sequence and Alignment Scoring function and BLOSUM matrix

rounding factor

SLIDE 28

Sequence and Alignment Affine Gap Penalty

SLIDE 29

Pattern Matching

SLIDE 30

Pattern Matching Naive Approach

K: number of patterns
N: average length of pattern
M: length of the query string

Running Time: O(KMN)

SLIDE 31

Pattern Matching Keyword Tree

K: number of patterns
N: average length of pattern
M: length of the query string

Running Time: O(KN + NM)

SLIDE 32

Pattern Matching

K: number of patterns
N: average length of pattern
M: length of the query string

Running Time: O(KN + M)

Aho-Corasick

SLIDE 33

Pattern Matching

One more example:

http://blog.ivank.net/aho-corasick-algorithm-in-as3.html

Aho-Corasick

SLIDE 34

Pattern Matching

Fixed patterns with various query string… what if we have a fix string but different query patterns? compile the patterns -> compile the string

A different setting

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Pattern Matching

N: average length of pattern
M: length of the query string

Running time: O(M^2 + N) Build a keyword tree: {abcabx, bcabx, cabx, abx, bx, x}

Suffix Tree for {abcabx}

SLIDE 36

Pattern Matching

N: average length of pattern
M: length of the query string

Running time: O(M^2 + N) O(M + N) if do Ukkonen Algo. but no required!

Suffix Tree for {abcabx}

SLIDE 37

Review Session I CS 466 Wesley Wei Qian March 10th 2020 Midterm - - PowerPoint PPT Presentation

Review Session I

Good luck!