Difference between revisions of "Sequence-based mutation analysis BCKDHA"

From Bioinformatikpedia
(Subset of mutations)
(Polyphen2)
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==Polyphen2==
 
==Polyphen2==
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{|border="1"
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!rowspan="2" | Position
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!rowspan="2" | AA1/AA2
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!colspan="4"| HumDiv
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!colspan="4" |HumVar
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|-
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!prediction
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!Score
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!Sensitivity
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!Specificity
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!prediction
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!Score
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!Sensitivity
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!Specificity
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|-
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|29||G/E||benign||0.025||0.96||0.80||benign ||0.018||0.96||0.52
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|-
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|125||Q/E||possibly damaging||0.759||0.85||0.93||benign||0.285||0.87|| 0.75
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|-
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|166||Y/N||probably damaging||0.997||0.40||0.98||probably damaging|| 0.964|| 0.59||0.93
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|-
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|249||G/S||benign||0.145||0.93||0.86||benign||0.292|| 0.86||0.75
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|-
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|264||C/W||probably damaging||1.000||0.00||1.00||probably damaging||1.000||0.00|| 1.00
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|-
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|265||R/W||probably damaging||1.000||0.00|| 1.00||probably damaging|| 1.000|| 0.00||1.00
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|-
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|326||I/T||probably damaging||0.997|| 0.40||0.98||probably damaging||0.998 || 0.16||0.99
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|-
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|361||I/V||benign|| 0.039||0.95|| 0.82||benign ||0.178||0.89|| 0.70
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|-
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|409||F/C||probably damaging || 0.998|| 0.27||0.99||probably damaging || 0.939 || 0.64|| 0.92
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|-
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|438||Y/N||probably damaging ||1.000|| 0.00|| 1.00||probably damaging || 0.987 || 0.49||0.96
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|}
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Revision as of 20:00, 21 June 2011

Subset of mutations

Reference amino acid Mutated amino acid BLOSUM62 PAM1 PAM250 Secondary Structure
Position Residue Properties Structure Residue Properties Structure
29 G tiny, small E charged, polar C
125 Q acidic, polar E charged, polar C
166 Y hydrophobic, aromatic, polar N acidic, polar, small H
249 G tiny, small S polar, small, tiny, hydroxylic H
264 C sulphur containing, hydrophobic, tiny, small, polar W hydrophobic, aromatic, polar E
265 R charged, positive (basic), polar W E
326 I T E
361 I V H
409 F C C
438 Y N C

Annotation: H = helix, E = beta-sheet, C = coil

PSSM

PsiBlast was run using the following command: blastpgp -i sequence.fasta -j 5 -d /data/blast/nr/nr -C profile.ckp

SNAP

SIFT

Polyphen2

Position AA1/AA2 HumDiv HumVar
prediction Score Sensitivity Specificity prediction Score Sensitivity Specificity
29 G/E benign 0.025 0.96 0.80 benign 0.018 0.96 0.52
125 Q/E possibly damaging 0.759 0.85 0.93 benign 0.285 0.87 0.75
166 Y/N probably damaging 0.997 0.40 0.98 probably damaging 0.964 0.59 0.93
249 G/S benign 0.145 0.93 0.86 benign 0.292 0.86 0.75
264 C/W probably damaging 1.000 0.00 1.00 probably damaging 1.000 0.00 1.00
265 R/W probably damaging 1.000 0.00 1.00 probably damaging 1.000 0.00 1.00
326 I/T probably damaging 0.997 0.40 0.98 probably damaging 0.998 0.16 0.99
361 I/V benign 0.039 0.95 0.82 benign 0.178 0.89 0.70
409 F/C probably damaging 0.998 0.27 0.99 probably damaging 0.939 0.64 0.92
438 Y/N probably damaging 1.000 0.00 1.00 probably damaging 0.987 0.49 0.96



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