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Motif detection and Screening

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(1)

Exercises

Motif detection and Screening

09112006

(2)

Exercises OVERVIEW

Sequence

Identify homologs Select Intergenics Phylogenetic

footprinting

Genome wide screening

Blast

INCLUsive

Motif Sampler/

RSA

Motif Scanner/

RSA

(3)

Exercises SELECTION INTERGENIC SEQUENCES

(4)

Exercises SELECTION INTERGENIC SEQUENCES

(5)

Exercises SELECTION INTERGENIC SEQUENCES

(6)

Exercises

Motif Detection

(7)

Exercises OVERVIEW

Sequence

Identify homologs Select Intergenics Phylogenetic

footprinting

Genome wide screening

Blast

INCLUsive

Motif Sampler/

RSA

Motif Scanner/

RSA

(8)

Exercises

Motif Detection: Gibbs

(9)

Exercises

Motif Detection: Gibbs

(10)

Exercises

Motif Detection: Gibbs

(11)

Exercises

Motif Detection: Gibbs

Regular expression

Consensus: TTGATCTAGATCAA

(12)

Exercises

Motif Detection: RSA

(13)

Exercises

Motif Detection: RSA

(14)

Exercises

Motif Detection: RSA

(15)

Exercises

Motif Detection: RSA

(16)

Exercises

Motif Detection: RSA

(17)

Exercises OVERVIEW

Sequence

Identify homologs Select Intergenics Phylogenetic

footprinting

Genome wide screening

Blast

INCLUsive

Motif Sampler/

RSA

Motif Scanner/

RSA

(18)

Exercises

CONSENSUS

(19)

Exercises

CONSENSUS

(20)

Exercises

REGULAR EXPRESSION

(21)

Exercises

MotifScanner

(22)

Exercises

MotifScanner

start stop

score consensus hit

(23)

Exercises

EcoCYC

(24)

Exercises

EcoCYC

cydA encodes a terminal

oxidase

Its regulation by FNR was to be expected

(25)

Exercises

EcoCYC

yejG is a novel protein with unknown function But from in silico analysis you know it might be regulated by O2

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