Difference between revisions of "PsiPred of Mutated PAH"

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(Created page with "Original: Conf: 201354166889999179999940599256899999985310343111235866888999 Pred: CCCEEECCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC AA: NLTHIESRPSRLKKD'''E'''YEF…")
 
 
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We fed the mutated sequences to PsiPred in the hope to maybe see a collapse of secondary structures in the prediction after the sequence change.
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Unfortunately, the structure at the SNP sites never changes, in most cases even the confidence only drops one point, if at all. Interestingly, the Leu255Ser mutation introduces a new short beta sheet from 265 to 268 overlapping a real sheet from 262 to 265 overlooked by PsiPred in the unmutated sequence. As it is, we do not gain any usable information from this approach.
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Original:
 
Original:
 
Conf: 201354166889999179999940599256899999985310343111235866888999
 
Conf: 201354166889999179999940599256899999985310343111235866888999
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130 140 150 160 170 180
 
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Conf: 998976897755323124766568999997155678876466543101257788854345
Conf: 998941687654213034766568999998845665555456442102357888754344
 
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Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
 
AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARSKQFADIAYNYRHG'''H'''PIPRVEYM
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AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHG'''H'''PIPRVEYM
 
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130 140 150 160 170 180
   
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AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIP'''W'''PFSVRYDPYTQR
 
AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIP'''W'''PFSVRYDPYTQR
 
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[[Category: Phenylketonuria 2012]]

Latest revision as of 13:04, 29 August 2012

We fed the mutated sequences to PsiPred in the hope to maybe see a collapse of secondary structures in the prediction after the sequence change. Unfortunately, the structure at the SNP sites never changes, in most cases even the confidence only drops one point, if at all. Interestingly, the Leu255Ser mutation introduces a new short beta sheet from 265 to 268 overlapping a real sheet from 262 to 265 overlooked by PsiPred in the unmutated sequence. As it is, we do not gain any usable information from this approach.

Original:

Conf: 201354166889999179999940599256899999985310343111235866888999
Pred: CCCEEECCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
  AA: NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
              70        80        90       100       110       120

Mutated: (76/87)

Conf: 200233276788999437999722689057899999986420342112235867888899
Pred: CEEEEECCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
  AA: NLTHIESRPSRLKKDGYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
              70        80        90       100       110       120
Conf: 201233375789999449999832798135799999874402452000245866898999
Pred: CCCEEECCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
  AA: NLTHIESRPSRLKKDEYEFFTHLDKRRLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
              70        80        90       100       110       120


Original:

Conf: 998942797754324124776678999997156789986477665321037888854356
Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
  AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
             130       140       150       160       170       180

Mutatated: (158/172)

Conf: 998966897754224213566678999998545564466544311000136778854356
Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
  AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARQKQFADIAYNYRHGQPIPRVEYM
             130       140       150       160       170       180
Conf: 998976897755323124766568999997155678876466543101257788854345
Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
  AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGHPIPRVEYM
             130       140       150       160       170       180

Original:

Conf: 698338877726578753203013000236999999999971488731798766796579
Pred: EEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHH
  AA: RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
             250       260       270       280       290       300

Mutated: (243/255/276)

Conf: 698348887726678764300045000003799999999952588631898866796579
Pred: EEEECCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHH
  AA: RLQPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
             250       260       270       280       290       300
Conf: 698328988826467542114022331005999999999962488731898866796579
Pred: EEEECCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHH
  AA: RLRPVAGLLSSRDFSGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
             250       260       270       280       290       300
Conf: 698348987726578763301033000125999999999961488631898866796579
Pred: EEEECCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHH
  AA: RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPVYTPEPDICHELLGHVPLFSDRSFA
             250       260       270       280       290       300

Original:

Conf: 999999663228997899999876302467746320894046212201232321101379
Pred: HHHHHHHHHHCCCCHHHHHHHHHHHHEEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCC
  AA: QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
             310       320       330       340       350       360

Mutated: (337)

Conf: 999999664228996899999774213578733211794136223212333443211379
Pred: HHHHHHHHHHCCCCHHHHHHHHHHHEEEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCC
  AA: QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQVDSIKAYGAGLLSSFGELQYCLSE
             310       320       330       340       350       360

Original:

Conf: 995113695433043465577654178737987999999998850899974334662007
Pred: CCCCCCCCHHHHHCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCCE
  AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
             370       380       390       400       410       420

Mutated: (408)

Conf: 995124695433043465577654178737987999999987703799961122453227
Pred: CCCCCCCCHHHHHCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCCE
  AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPWPFSVRYDPYTQR
             370       380       390       400       410       420