Difference between revisions of "Rs4777505"

From Bioinformatikpedia
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'''Conservation analysis with multiple alignments'''
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=== Conservation Analysis with Multiple Alignments ===
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[[Image:mut_1.png|thumb|center|600px|Mutation in the multiple alignment]]
 
[[Image:mut_1.png|thumb|center|600px|Mutation in the multiple alignment]]
   
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----
'''Secondary structure mutation analysis'''
 
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=== Secondary structure mutation analysis ===
   
 
JPred:
 
JPred:
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----
   
'''SNAP Prediction'''
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=== SNAP Prediction ===
   
 
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A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs4777505_SNAP here]]
 
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs4777505_SNAP here]]
   
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----
'''SIFT Prediction'''
 
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=== SIFT Prediction ===
   
 
SIFT Matrix:<br>
 
SIFT Matrix:<br>
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<br><br>
 
<br><br>
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'''Polyphen2 Prediction'''
 
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----
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=== Polyphen2 Prediction ===
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| [[Image:mut_1_humdiv.png|thumb|450px|HumDiv prediction]]
 
| [[Image:mut_1_humdiv.png|thumb|450px|HumDiv prediction]]

Revision as of 16:10, 23 June 2011

Pysicochemical Properities

Asn Ser consequences
polar, small, hydrophilic, negatively charged polar, tiny, hydrophilic, neutral Both amino acids are polar and hydrophilic. Ser is tiny, Asn therefore is a small amino acid. The biggest difference between these two amino acid is, that Asn is negatively charged and Ser is neutral. But this is not that big difference and therefore we suggest, that this mutation do not delete the structure and function of the protein.



Visualisation of the Mutation

picture original aa picture mutated aa combined picture
Amino acid Asparagine
Amino acid Serine
Picture which visualize the mutation

Subsitution Matrices values

PAM 1 Pam 250 BLOSOUM 62
value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution
20 36 (Asp) 0 (Cys, Met) 5 7 (Asp) 2 (Cys, Leu, Phe, Trp) 1 1 (Asp, His, Ser) -4 (Trp)

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary structure mutation analysis

JPred:
CCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCEEEEECCCEEEEECCCCCCC...
PsiPred:
CHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEEECCCEEEEECCCCCCC...

Comparison with the real structure:

Mutation at position 29
Mutation at position 29 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
S Neutral 8 96%

A detailed list of all possible substitutions can be found [here]


SIFT Prediction

SIFT Matrix:
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.

Sift legend.png
29 sift.png.png

SIFT Table
Threshold for intolerance is 0.05.
Amino acid color code: nonpolar, uncharged polar, basic, acidic.
Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.



Predict Not ToleratedPositionSeq RepPredict Tolerated
w29N0.78cfMHiYpVgLRNdQTASKE




Polyphen2 Prediction

HumDiv prediction
HumVar prediction