Supplementary Data

chirpskulkInternet and Web Development

Nov 3, 2013 (3 years and 9 months ago)

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BLAST

a glimpse under the hood

Prospero:



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
-
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 stuff

As dreams are made on; and our little life

Is rounded with a sleep.


find this

Prospero:



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
-
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 stuff

As dreams are made on; and our little life

Is rounded with a sleep.


in here

Prospero:



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
-
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 stuff

As

dreams
are

made on; and our little life

Is

rounded
with a

sleep.


cloud
-
capp'd tow'rs

cloud
-
capp
e
d tow
e
rs

cloudcapp'd tow
e
rs


cloud
-
ti
pp
e
d tow
el
s

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
lik
e 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
-
capp
e
d tow
e
rs

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

in
substantial 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

+

+

+

+

+

+

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

fa
ded,

vision, The cloud
-
capped towers, the gorgeous palaces, The

+

+

+

+

+

+

Natural

scenario

The

1 Panda genome


1 gene


in

~
2.30

 gigabases (Gb)


~
1

kilobase (kb)

in

in

GenBank

Panda genome

Describe the principle

Describe the steps

Discuss the concepts

Use 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
, and

Are

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 stuff

As

dreams
are

made on; and our little life

Is

rounded
with a

sleep.


1.

vifnknvikctgesqtgntgggqagntggdqagstggspqgstgaspqgst
gaspqgstgasqpgssepsnpvssghsvstvsvsqtstssekqdtiqvks
allkdymglkvtgpcnenfimflvphiyidvdtedtnielrttlkktnnaisfesn
sgslekkkyvklpsngttgeqgsstgtvrgdtepisd
sssssssssssssss
ssssssssssss
eslpangpdsptvkpprnlqnicetgknfklvvyikent

low complexity

2.

PAQILWQEDARRKGSM

PAQ

P
AQI

PA
QIL

PAQ
ILW

PAQI
LWQ

PAQIL
WQE

PAQILW
QED…

build word list

nt words = 11 characters

aa words = 3 characters

Biology

BLAST

3.
&

4.

in

3.

evaluate matching words

PAQ

P
AQI

PA
QIL

PAQ
ILW

PAQI
LWQ

PAQIL
WQE

PAQILW
QED…

QVL

QIA

RIL …

8000 possible scores

20 x 20 x 20

e.g. score with BLOSUM

cloud
-
capp'd tow'rs

cloud
-
capp
e
d tow
e
rs

cloudcapp'd tow
e
rs


cloud
-
ti
pp
e
d tow
el
s

QVL

QIA

RIL …

QIL

H

K

R

E

D

N

Q

P

I

V

L

M

F

W

Y

S

T

C

G

A

Hydrophobic

Hydrophilic

Aromatic

Small

Charged

cyclic side
-
chain

Amines

Aliphatic

-

OH

retain

high
-
scoring words

Q
VL

Q
I
A

R
IL



Q
IL

5 + 4 + 4

5 + 3 + 4

5 + 4
-

1

BLOSUM62

1 + 4 + 4

T

= 10

8000 words


捡‵0

4.

What about nucleotide words?

5.

Repeat 3. and 4.

for each word

listed

A 50
n

polypeptide will

yield ~12,500 words

6.

create search tree

QIL

QVL

QII

NIL

Q

Q

N

QV

QI

QII

QIL

V

I

L

I

QVL

L

N

NI

NIL

I

L

7.

plant seeds

Query

high
-
scoring words in position
n

Database

n
= 3

光L,

QVL



Exact matches

8
v
1

grow HSPs

+

+

+

+

+

+

stop when maximal score

drops 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

+

+

+

+

+

+

The image of “
cloud
-
capped towers
”, unites ethereality and might

vision, The cloud
-
capped towers, the gorgeous palaces, The

-

-

-

-

-

-

-

+

-

-

-

+

8
v
2

grow HSPs

use words at
T



longer word list

Query sequence

Database sequence

X

X

X

X

X

X

X

A

8
v
2

grow HSPs

extend ‘close’ words as one

X

X

A

A

9.

filter HSPs

HSP

HSP

HSP

HSP

S

cut
-
off score

≥ S

≤ S

10.

determine


score significance

Could 2 random sequences

with the lengths of the query

and database resp. score

achieve the ≥ HSP score?

10.

determine


score significance

DB

Query

World of randomness

S

S*

S**

S***

S****

S*****

S******

10.

determine


score significance

K,
λ

calculated for the scoring matrix

m’ effective length of database seq

n’ effective length of query seq

10.

determine


score significance

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

13.

Deliver results

E

user selected cut
-
off score

< E

> E

BLAST

A practical example

Mutation

*

*

*

PCR

Primer binding sites

Transposon mutagenesis

*

*

PCR

Seq 1

Seq 2

BLAST

Self
-
study