BLAST

1
a glimpse under the hood
BLAST
2
Prospero Our revels now are ended. These our
actors,As I foretold you, were all spirits,
andAre melted into air, into thin airAnd like
the baseless fabric of this vision,The
cloud-capp'd tow'rs, the gorgeous palaces,The
solemn temples, the great globe itself,Yea, all
which it inherit, shall dissolve,And, like this
insubstantial pageant faded,Leave not a rack
behind. We are such stuffAs dreams are made on
and our little lifeIs rounded with a sleep.
find this
3
Prospero Our revels now are ended. These our
actors,As I foretold you, were all spirits,
andAre melted into air, into thin airAnd like
the baseless fabric of this vision,The
cloud-capp'd tow'rs, the gorgeous palaces,The
solemn temples, the great globe itself,Yea, all
which it inherit, shall dissolve,And, like this
insubstantial pageant faded,Leave not a rack
behind. We are such stuffAs dreams are made on
and our little lifeIs rounded with a sleep.
in here
4
Prospero Our revels now are ended. These our
actors,As I foretold you, were all spirits,
andAre melted into air, into thin airAnd like
the baseless fabric of this vision,The
cloud-capp'd tow'rs, the gorgeous palaces,The
solemn temples, the great globe itself,Yea, all
which it inherit, shall dissolve,And, like this
insubstantial pageant faded,Leave not a rack
behind. We are such stuffAs dreams are made on
and our little lifeIs rounded with a sleep.
5
cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
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cloud-capped towers
cloud-capp'd tow'rs
Our revels now are ended. These our actors, As I
foretold you, were all spirits, and Are melted
into air, into thin air And like the baseless
fabric of this vision, The cloud-capped towers,
the gorgeous palaces, The solemn temples, the
great globe itself, Yea, all which it inherit,
shall dissolve, And, like this insubstantial
pageant faded,
7
cloud-capped towers
r And like the baseless fabric of this vision,
The cloud-capped towers, the gorgeous palaces,
The solemn temples, the great globe itself, Yea,
all which it inherit, shall dissolve, And, like
this insubstantial pageant faded,
8
vision, The cloud-capped towers, the gorgeous
palaces, The
r And like the baseless fabric of this vision,
The cloud-capped towers, the gorgeous palaces, The






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vision, The cloud-capped towers, the gorgeous
palaces, The
r And like the baseless fabric of this vision,
The cloud-capped towers, the gorgeous palaces,
The solemn temples, the great globe itself, Yea,
all which it inherit, shall dissolve, And, like
this insubstantial pageant faded,






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The
Natural
scenario
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(No Transcript)
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1 gene
in
1 Panda genome
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1 kilobase (kb)
in
2.30 ?gigabases (Gb)
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in
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Panda genome
GenBank
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Learning goals BLAST
Describe the principle Describe the steps Discuss
the concepts Use BLAST!
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????s??
Heuristic
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The algorithm
in 13 steps
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Information
reduction in uncertainty
degree of surprise
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Prospero Our revels now are ended. These our
actors,As I foretold you, were all spirits,
andAre melted into air, into thin airAnd like
the baseless fabric of this vision,The
cloud-capp'd tow'rs, the gorgeous palaces,The
solemn temples, the great globe itself,Yea, all
which it inherit, shall dissolve,And, like this
insubstantial pageant faded,Leave not a rack
behind. We are such stuffAs dreams are made on
and our little lifeIs rounded with a sleep.
21
(No Transcript)
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vifnknvikctgesqtgntgggqagntggdqagstggspqgstgaspqgs
tgaspqgstgasqpgssepsnpvssghsvstvsvsqtstssekqdtiqvk
sallkdymglkvtgpcnenfimflvphiyidvdtedtnielrttlkktnn
aisfesnsgslekkkyvklpsngttgeqgsstgtvrgdtepisdssssss
ssssssssssssssssssssseslpangpdsptvkpprnlqnicetgknf
klvvyikent
low complexity
1.
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PAQILWQEDARRKGSM
PAQ
PAQI
nt words 11 characters aa words 3 characters
PAQIL
PAQILW
PAQILWQ
PAQILWQE
PAQILWQED
2.
build word list
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Biology
in
BLAST
3. 4.
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evaluate matching words
e.g. score with BLOSUM
PAQ
PAQI
PAQIL
PAQILW
QVL
PAQILWQ
QIA
PAQILWQE
RIL
PAQILWQED
3.
20 x 20 x 20
8000 possible scores
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cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
QIL
QVL
QIA
RIL
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Small
P
G
cyclic side-chain
A
C
Aromatic
S
- OH
T
Y
Amines
W
M
H
K
N
F
E
Aliphatic
R
D
Q
I
V
L
Charged
Hydrophobic
Hydrophilic
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BLOSUM62
8000 words ? ca 50
QIL
5 4 4
T 10
QVL
5 3 4
QIA
5 4 - 1
RIL
1 4 4
4.
retain high-scoring words
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What about nucleotide words?
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Repeat 3. and 4. for each word listed
5.
A 50n polypeptide will yield 12,500 words
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create search tree
QIL
Q
N
QVL
QII
Q
N
NIL
V
I
I
QV
QI
NI
6.
L
I
L
L
QII
QIL
QVL
NIL
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plant seeds
Query
high-scoring words in position n
n 3 ?QIL, QVL
Exact matches
7.
Database
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stop when maximal score drops by a threshold X






8v1
grow HSPs
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vision, The cloud-capped towers, the gorgeous
palaces, The
r And like the baseless fabric of this vision,
The cloud-capped towers, the gorgeous palaces, The






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vision, The cloud-capped towers, the gorgeous
palaces, The
The image of cloud-capped towers, unites
ethereality and might
-
-

-
-
-
-
-

-
-
-
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use words at T ? longer word list
X
X
A
X
X
Query sequence
X
X
X
8v2
Database sequence
grow HSPs
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extend close words as one
A
X
X
8v2
A
grow HSPs
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filter HSPs
HSP
HSP
HSP
HSP
9.
S
S
S
cut-off score
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determine score significance
Could 2 random sequences with the lengths of the
query and database resp. score achieve the HSP
score?
10.
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determine score significance
DB
S
Query
S
S
10.
S
S
S
World of randomness
S
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determine score significance
10.
K, ? calculated for the scoring matrix
m effective length of database seq
n effective length of query seq
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determine score significance
10.
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Extend 2 HSPs
S
65
40
52
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Poisson
40 lt 45
11.
Sum of scores
(6540) gt (5245)
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Perform Smith-Waterman (local) alignments
BLAST
BLAST2
12.
Calculate bit score (S) and E-value of each SW
alignment
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Deliver results
lt E
gt E
13.
E
user selected cut-off score
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A practical example
BLAST
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Mutation
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Primer binding sites
PCR
Transposon mutagenesis
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PCR
Seq 1
Seq 2
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Self-study
BLAST