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a glimpse under the hood. BLAST. Prospero: - PowerPoint PPT Presentation
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BLASTa glimpse under the hood
Prospero:
Our revels now are ended. These our actors,As I foretold you, were all spirits, andAre melted into air, into thin air:And 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
Prospero:
Our revels now are ended. These our actors,As I foretold you, were all spirits, andAre melted into air, into thin air:And 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
Prospero:
Our revels now are ended. These our actors,As I foretold you, were all spirits, andAre melted into air, into thin air:And 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.
cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
cloud-capp'd tow'rsOur 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,
cloud-capped towers
cloud-capped towersr: 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,
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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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, vision, The cloud-capped towers, the gorgeous palaces, The
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Naturalscenario
The
1 Panda genome
1 gene
in
~ 2.30 gigabases (Gb)
~ 1 kilobase (kb)
in
in
GenBank
Panda genome
Describe the principleDescribe the stepsDiscuss the conceptsUse BLAST!
Learning goals [BLAST]
Heuristic
Εὑρίσκω
The algorithm
in 13 steps
Information
degree of surprise
reduction in uncertainty
Prospero:
Our revels now are ended. These our actors,As I foretold you, were all spirits, andAre melted into air, into thin air:And 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.
ppH
1log)( 2
1.
vifnknvikctgesqtgntgggqagntggdqagstggspqgstgaspqgstgaspqgstgasqpgssepsnpvssghsvstvsvsqtstssekqdtiqvksallkdymglkvtgpcnenfimflvphiyidvdtedtnielrttlkktnnaisfesnsgslekkkyvklpsngttgeqgsstgtvrgdtepisdssssssssssssssssssssssssssseslpangpdsptvkpprnlqnicetgknfklvvyikent
low complexity
01
1log)1( 2 H
2.
PAQILWQEDARRKGSMPAQPAQIPAQILPAQILWPAQILWQPAQILWQEPAQILWQED…
build word list
nt words = 11 charactersaa words = 3 characters
Biology
BLAST
3. & 4.
in
3.
evaluate matching wordsPAQPAQIPAQILPAQILWPAQILWQPAQILWQEPAQILWQED…
QVLQIARIL …
8000 possible scores
20 x 20 x 20
e.g. score with BLOSUM
cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
QVLQIARIL …
QIL
H KR
ED
N
Q
P
I V L
M FW
YS
T
C
GA
Hydrophobic
Hydrophilic
Aromatic
Small
Charged
cyclic side-chain
Amines
Aliphatic
- OH
retain high-scoring words
QVLQIARIL …
QIL 5 + 4 + 45 + 3 + 45 + 4 - 1
BLOSUM62
1 + 4 + 4
T = 10
8000 words ca 50
4.
What about nucleotide words?
5.
Repeat 3. and 4.for each word
listedA 50n polypeptide will yield ~12,500 words
6.
create search treeQIL
QVL
QII
NIL
Q
Q N
QV QI
QII QIL
V I
LI
QVL
L
N
NI
NIL
I
L
7.
plant seedsQuery
high-scoring words in position n
Database
n = 3 QIL, QVL …
Exact matches
8v1 grow HSPs
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stop when maximal scoredrops by a threshold X
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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The image of “cloud-capped towers”, unites ethereality and mightvision, The cloud-capped towers, the gorgeous palaces, The
- ---
--
- +-
-- +
8v2 grow HSPs
use words at T longer word list
Qu
ery
se
qu
en
ce
Database sequence
X
X
XX
X
X
XA
8v2 grow HSPs
extend ‘close’ words as one
XX
A
A
9.
filter HSPs
HSP
HSP
HSP
HSP
Scut-off score
≥ S≤ S
10.
determine score significance
Could 2 random sequenceswith the lengths of the queryand database resp. scoreachieve the ≥ HSP score?
10.
determine score significance
DB
Query
World of randomness
S
S*
S**
S***
S****
S*****
S******
10.
determine score significance
)exp(1)( )( xexSp
''log nKm
K, λ calculated for the scoring matrix
m’ effective length of database seq
n’ effective length of query seq
10.
determine score significance
DxspeE )(1
11.
Extend ≥2 HSPs
S 65 40 52 45
Poisson
Sum of scores (65+40) > (52+45)
40 < 45
12.
Perform Smith-Waterman(local) alignments
BLAST
BLAST2
Calculate bit score (S’) and E-value of each SW alignment
e'' S-nkmE
13.
Deliver results
Euser selected cut-off score
< E> E
BLASTA practical example
Mutation
*
*
*
PCR
Primer binding sites
Transposon mutagenesis
*
*PCR
Seq 1 Seq 2
BLASTSelf-study
