Difference between revisions of "PsiPred of Mutated PAH"
From Bioinformatikpedia
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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: |
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Conf: 201354166889999179999940599256899999985310343111235866888999 |
Conf: 201354166889999179999940599256899999985310343111235866888999 |
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| + | Conf: 998976897755323124766568999997155678876466543101257788854345 |
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| − | Conf: 998941687654213034766568999998845665555456442102357888754344 |
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| + | Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC |
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| − | Pred: CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC |
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| − | AA: |
+ | AA: FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHG'''H'''PIPRVEYM |
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AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIP'''W'''PFSVRYDPYTQR |
AA: KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIP'''W'''PFSVRYDPYTQR |
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| + | [[Category: Phenylketonuria 2012]] |
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Latest revision as of 12:04, 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
