BLAST
description
Transcript of BLAST
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BLASTa glimpse under the hood
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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 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
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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 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
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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 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.
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cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
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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
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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,
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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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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
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1 Panda genome
1 gene
in
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~ 2.30 gigabases (Gb)
~ 1 kilobase (kb)
in
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in
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GenBank
Panda genome
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Describe the principleDescribe the stepsDiscuss the conceptsUse BLAST!
Learning goals [BLAST]
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Heuristic
Εὑρίσκω
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The algorithm
in 13 steps
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Information
degree of surprise
reduction in uncertainty
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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 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.
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ppH
1log)( 2
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1.
vifnknvikctgesqtgntgggqagntggdqagstggspqgstgaspqgstgaspqgstgasqpgssepsnpvssghsvstvsvsqtstssekqdtiqvksallkdymglkvtgpcnenfimflvphiyidvdtedtnielrttlkktnnaisfesnsgslekkkyvklpsngttgeqgsstgtvrgdtepisdssssssssssssssssssssssssssseslpangpdsptvkpprnlqnicetgknfklvvyikent
low complexity
01
1log)1( 2 H
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2.
PAQILWQEDARRKGSMPAQPAQIPAQILPAQILWPAQILWQPAQILWQEPAQILWQED…
build word list
nt words = 11 charactersaa words = 3 characters
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Biology
BLAST
3. & 4.
in
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3.
evaluate matching wordsPAQPAQIPAQILPAQILWPAQILWQPAQILWQEPAQILWQED…
QVLQIARIL …
8000 possible scores
20 x 20 x 20
e.g. score with BLOSUM
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cloud-capp'd tow'rs
cloud-capped towers
cloudcapp'd towers
cloud-tipped towels
QVLQIARIL …
QIL
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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
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retain high-scoring words
QVLQIARIL …
QIL 5 + 4 + 45 + 3 + 45 + 4 - 1
BLOSUM62
1 + 4 + 4
T = 10
8000 words ca 50
4.
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What about nucleotide words?
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5.
Repeat 3. and 4.for each word
listedA 50n polypeptide will yield ~12,500 words
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6.
create search treeQIL
QVL
QII
NIL
Q
Q N
QV QI
QII QIL
V I
LI
QVL
L
N
NI
NIL
I
L
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7.
plant seedsQuery
high-scoring words in position n
Database
n = 3 QIL, QVL …
Exact matches
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8v1 grow HSPs
++ ++
++
stop when maximal scoredrops by a threshold X
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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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The image of “cloud-capped towers”, unites ethereality and mightvision, The cloud-capped towers, the gorgeous palaces, The
- ---
--
- +-
-- +
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8v2 grow HSPs
use words at T longer word list
Qu
ery
se
qu
en
ce
Database sequence
X
X
XX
X
X
XA
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8v2 grow HSPs
extend ‘close’ words as one
XX
A
A
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9.
filter HSPs
HSP
HSP
HSP
HSP
Scut-off score
≥ S≤ S
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10.
determine score significance
Could 2 random sequenceswith the lengths of the queryand database resp. scoreachieve the ≥ HSP score?
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10.
determine score significance
DB
Query
World of randomness
S
S*
S**
S***
S****
S*****
S******
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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
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10.
determine score significance
DxspeE )(1
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11.
Extend ≥2 HSPs
S 65 40 52 45
Poisson
Sum of scores (65+40) > (52+45)
40 < 45
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12.
Perform Smith-Waterman(local) alignments
BLAST
BLAST2
Calculate bit score (S’) and E-value of each SW alignment
e'' S-nkmE
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13.
Deliver results
Euser selected cut-off score
< E> E
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BLASTA practical example
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Mutation
*
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*
*
PCR
Primer binding sites
Transposon mutagenesis
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*
*PCR
Seq 1 Seq 2
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BLASTSelf-study