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Exemple de Calcul D'une Matrice de Poids

This document describes calculating a weight matrix for DNA sequences. It provides two 10x5 matrices showing the frequency of nucleotides at each position of 5 pre-aligned sequences. A consensus sequence is determined by taking the most frequent nucleotide at each position. The consensus sequence is then CCCGGAAACG with a score of 1.96.

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Ahmed DZ
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89 views5 pages

Exemple de Calcul D'une Matrice de Poids

This document describes calculating a weight matrix for DNA sequences. It provides two 10x5 matrices showing the frequency of nucleotides at each position of 5 pre-aligned sequences. A consensus sequence is determined by taking the most frequent nucleotide at each position. The consensus sequence is then CCCGGAAACG with a score of 1.96.

Uploaded by

Ahmed DZ
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Exemple de calcul d’une matrice de poids

G C C G G A A G T G

A C C G G A A G C A

G C C G G A T G C A

C A A G G A C G A C

C C C G G A A G T G

1 2 3 4 5 6 7 8 9 10
1 2 3 4 5 6 7 8 9 10 Tot
A 1 1 1 0 0 5 3 0 1 2 14
C 2 4 4 0 0 0 1 0 2 1 14
G 2 0 0 5 5 0 0 5 0 2 19
T 0 0 0 0 0 0 1 0 2 0 3
Tot 5 5 5 5 5 5 5 5 5 5 50

fi 1 2 3 4 5 6 7 8 9 10 Fi
0.071 0.071 0.071 0.000 0.000 0.357 0.214 0.000 0.071 0.143 14/50
A:ai/14 =0.28
0.143 0.286 0.286 0.000 0.000 0.000 0.071 0.000 0.143 0.071 14/50
C:ci/14 =0.28
0.105 0.000 0.000 0.263 0.263 0.000 0.000 0.263 0.000 0.105 19/50
G:gi/19 =0.38
0.000 0.000 0.000 0.000 0.000 0.000 0.333 0.000 0.666 0.000 3/50=
T:ti/3 0.06

A : fi/Fi 0,254 0,254 0,254 0,000 0,000 1,275 0,764 0,000 0,254 0,511

C : fi/Fi 0,511 1,021 1,021 0 0 0 0,254 0 0,511 0,254

G : fi/Fi 0,376 0 0 0,692 0,692 0 0 0,692 0 0,376

T : fi/Fi 0,000 0,000 0,000 0,000 0,000 0,000 5,550 0,000 11,1 0,000
Pour normaliser les valeurs prendre : Ln (valeurs fi/Fi)

A -1,370 -1,370 -1,370 ∞ ∞ 0,243 -0,269 ∞ -1,370 -0,671


C -0,671 0,021 0,021 ∞ ∞ ∞ -1,370 ∞ -0,671 -1,370

G -0,978 ∞ ∞ -0,368 -0,368 ∞ ∞ -0,368 ∞ -0,978

T ∞ ∞ ∞ ∞ ∞ ∞ 1,714 ∞ 2,407 ∞
Pénalité = -10 pour les valeurs incalculables (Ln (0))

A -1,370 -1,370 -1,370 -10 -10 0,243 -0,269 -10 -1,370 -0,671
C -0,671 0,021 0,021 -10 -10 -10 -1,370 -10 -0,671 -1,370
-10
G -0,978 -10 -10 -0,368 -0,368 -10 -10 -0,368 -0,978

T -10 -10 -10 -10 -10 -10 1,714 -10 2,407 -10

CONSENSUS C C C G G A T G T A

C(3)-G(2)-A-T-G-T-A
SCORE =-0,671+ 0,021+0,021-0,368-0,368+0,243+1,714-0,368+2,407-0,671 =1,96
A -1,370 -1,370 -1,370 -10 -10 0,243 -0,269 -10 -1,370 -0,671
C -0,671 0,021 0,021 -10 -10 -10 -1,370 -10 -0,671 -1,370
-10
G -0,978 -10 -10 -0,368 -0,368 -10 -10 -0,368 -0,978

T -10 -10 -10 -10 -10 -10 1,714 -10 2,407 -10

CONSENSUS C C C G G A T G T A
T C C G C A T G C A SCORE
-10 0,021 0,021 -0,368 -10 0,243 1,714 -0,368 -0,671 -0,671 -20,079

G C C G G A C G A A Score

-0,978 0,021 0,021 -0,368 -0,368 0,243 -1,370 -0,368 -1,370 -0,671 -5,208

Que conclure ?
G C C G G A A G T G

A C C G G A A G C A

G C C G G A T G C A

C A A G G A C G A C

C C C G G A A G T G

G C C G G A C G A A

La séquence qui contient ce motif peut être classée avec les 5 séquences pré-alignées

Forcer la recherche par :


ORFs
3’UTR
Homologie …

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