The document contains musical notation for the song "Nu cuoi trong mat em" by artist Tran Anh Tuan. It displays the musical staff with notes, tablature, lyrics, and other details about the song's performance. Specifically, it provides the sheet music across 10 pages with markings for pitch, rhythm, dynamics, and other musical elements to convey the song. The artist, song title, and other metadata are included at the top.
2016.09.28
TOPIC REVIEW
• Exam
• PS2 Sequence Alignment
• Command Line Blast
• PS1 Molecular Biology
• Personal Microbiome Project
CURRENTLY
LET’S NEGOTIATE
• Problem sets (4) - 10%
• Microbiome project - 20%
• Exam (1) - 20%
• Research project - 45%
• Participation - 5%
OR
• Problem sets (4) - 10%
• Microbiome project - 20%
• Exam 1 - 15%
• Exam 2 - 15%
• Research project - 35%
• Participation - 5%
PS2 SEQUENCE ALIGNMENT
PS2 SEQUENCE ALIGNMENT
RefSeqs, protein (experimentally supported)
On chromosome 17
Reverse strand
PRCD Progressive rod-cone degeneration
PS2: GLOBAL ALIGNMENT
BLOSUM62
• substitutions less penalized and are
preferred to gaps. There is also a
decrease in the level of identity.
BLOSUM80
• Substitutions more penalized and
gaps are favored.
PAM60
• Substitutions more penalized and gaps
are favored.
PAM250
• substitutions less penalized and are
preferred to gaps. There is also a
decrease in the level of identity.
PS2: LOCAL ALIGNMENT
SEQ1 A L S C V W M I P
SEQ2 A I S C M I P T
9 residues
8 residues
Create Matrix: length of seq1 + 1
x
length of seq2 + 1
Matrix 10 x 9
A L S C V W M I P
0 -2 -4 -6 -8 -10 -12 -14 -16 -18
-2
-4
-6
-8
-10
-12
-14
-16
A
I
S
C
M
I
P
T
Exercise: fill the scores of the alignment matrix
using the BLOSUM62 substitution matrix.
Gap opening penalty: -5
Gap extension penalty: -1
S V E T D
T
S
I
N
Q
E
T
Ala A 4
Arg R -1 5
Asn N -2 0 6
Asp D -2 -2 1 6
Cys C 0 -3 -3 -3 9
Gln Q -1 1 0 0 -3 5
Glu E -1 0 0 2 -4 2 5
Gly G 0 -2 0 -1 -3 -2 -2 6
His H -2 0 1 -1 -3 0 0 -2 8
Ile I -1 -3 -3 -3 -1 -3 -3 -4 -3 4
Leu L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4
Lys K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5
Met M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5
Phe F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6
Pro P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7
Ser S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4
Thr T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5
Trp W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11
Tyr Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7
Val V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4
A
la
A
rg
A
sn
A
sp
C
y
s
G
ln
G
lu
G
ly
H
is
Il
e
L
e
u
L
y
s
M
e
t
P
h
e
P
ro
S
e
r
T
h
r
T
rp
T
y
r
V
a
l
A R N D C Q E G H I L K M F P S T W Y V
Dynamical programming - global alignment
83
BLOSUM62
GAP COST: -2
At each cell, 3 scores are calculated:
• match score = diagonal cell score +
score from the substitution matrix.
• Vertical gap score = upper neighbor
+ gap cost
• Horizontal gap score = left neighbor
+ gap cost
• The highest score is retained and
the arrow is labelled
A L S C V W M I P
0 -2 -4 -6 -8 -10 -12 -14 -16 -18
-2
-4
-6
-8
-10
-12
-14
-16
A
I
S
C
M
I
P
T
Exercise: fill the scores of the alignment matrix
using the BLOSUM62 substitution matrix.
Gap opening penalty: -5
Gap extension penalty: -1
S V E T D
T
S
I
N
Q
E
T
A ...
7. A
D
F m
99
0
2
2
2
2
2
2
2
4
0
E
2
2
2
2
2
2
2
0
C m
2
3
2
3
2
2
F m
102
2
2
0
0
1
0
1
2
4
5
6
6
5
6
6
4
4
D
E
2
2
2
2
2
2
2
C m
105
2
0
2
3
2
3
2
2
1
2
2
0
0
0
1
6
2
6
5
6
6
4
D
F m
4
5
E
108
2
2
4
2
2
2
2
A
2
0
2
3
2
2
3
2
2
2
E
E
E E
E
A
A A A A A
0
0
1
2
2
0
0
0
1
2
2
0
0
0
1
2
2
0
0
0
1
2
2
0
0
2
2
2
0
0
2
2
2
0
2
1
0
0
0
1
2
F m F mF m m m m
F F F
111
0
2
2
2
0
2
2
2
0
0
1
2
2
0
0
2
2
2
0
0
2
2
2
0
X
X
X
X
X
0
2
2
2
0
2
2
2
4
2
2
2
4
X
X
X
X
2
2
2
4
2
2
2
4
2
2
2
4
7/10
8. A
A A
A A
A
0
2
2
2
0
0
2
2
2
0
0
2
2
2
0
0
2
2
2
0
F m F mF mF m m
F
115
2
3
2
0
2
3
2
0
2
3
2
0
2
3
2
0
2
3
2
0
2
3
2
0
0
0
1
2
2
0
0
0
1
2
2
0
D
0
0
1
2
2
0
0
0
1
2
2
0
0
0
1
2
2
0
0
0
1
2
2
0
0
2
2
2
0
E
X
X
X
X
X
2
2
2
4
2
2
2
4
X
X
X
X
2
2
2
4
2
2
2
4
C m
119
0
2
3
2
2
3
2
2
1
2
2
0
0
0
1
6
2
4
6
6
5
6
4
D
F m
5
E
122
4
2
2
2
2
2
2
2
C m
0
2
3
2
2
2
3
2
2
2
1
0
0
0
1
2
D
F m
125
6
5
4
6
6
5
6
4
4
2
2
2
2
2
2
2
2
2
0
2
3
2
2
2
3
2
A
128
2
1
0
0
1
2
1
0
0
1
2
0
0
2
0
0
2
2
2
3
2
0
0
2
3
0
2
3
0
3
2
8/10