Difference between revisions of "Predicting the Effect of SNPs (PKU)"

From Bioinformatikpedia
(Short Introduction)
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You could check them, if you like.. I put them together 5 minutes ago and already forgot, which are which. ;-)
 
You could check them, if you like.. I put them together 5 minutes ago and already forgot, which are which. ;-)
   
== Prediction Methods ==
+
== Investigated SNPS ==
===SIFT===
 
   
===PolyPhen2===
+
===GLU76GLY===
   
  +
From neg. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, non-hydrophilic, small.
===SNAP===
 
  +
  +
===SER87ARG===
  +
  +
From neutral, polar, slightly hydrophilic to pos. charged, polar, strongly hydrophilic.
  +
  +
===ARG158GLN===
  +
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  +
  +
===GLN172HIS===
  +
  +
From neutral, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic, ring-structure
  +
  +
===ARG243GLN===
  +
  +
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  +
  +
===LEU255SER===
  +
  +
From neutral, non polar, strongly hydrophobic to neutral, polar, slightly hydrophilic.
  +
  +
===MET276VAL===
  +
  +
From neutral, non-polar, hydrophobic to neutral, non-polar, strongly hydrophobic.
  +
  +
===ALA322GLY===
  +
  +
From neutral, non-polar, hydrophobic, small to neutral, non-polar, slightly hydrophilic, small.
  +
  +
===GLY337VAL===
  +
  +
From neutral, non-polar, slightly hydrophilic, small to neutral, non-polar, strongly hydrophobic, medium sized.
  +
  +
===ARG408TRP===
  +
  +
From pos. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, slightly hydrophilic, large.

Revision as of 17:21, 13 June 2012

Short Introduction

This week's task builds on the data gathered last week. We blindly choose 5 disease causing and 5 harmless SNPs and will try to predict their effect from the sequence change alone. You may find a detailed task description at the usual place and consult our task journal.

Our dataset

we propose the following dataset:

  • GLU76GLY
  • SER87ARG
  • GLN172HIS
  • ARG158GLN
  • ARG243GLN
  • LEU255SER
  • MET276VAL
  • ALA322GLY
  • GLY337VAL
  • ARG408TRP

You could check them, if you like.. I put them together 5 minutes ago and already forgot, which are which. ;-)

Investigated SNPS

GLU76GLY

From neg. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, non-hydrophilic, small.

SER87ARG

From neutral, polar, slightly hydrophilic to pos. charged, polar, strongly hydrophilic.

ARG158GLN

From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.

GLN172HIS

From neutral, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic, ring-structure

ARG243GLN

From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.

LEU255SER

From neutral, non polar, strongly hydrophobic to neutral, polar, slightly hydrophilic.

MET276VAL

From neutral, non-polar, hydrophobic to neutral, non-polar, strongly hydrophobic.

ALA322GLY

From neutral, non-polar, hydrophobic, small to neutral, non-polar, slightly hydrophilic, small.

GLY337VAL

From neutral, non-polar, slightly hydrophilic, small to neutral, non-polar, strongly hydrophobic, medium sized.

ARG408TRP

From pos. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, slightly hydrophilic, large.