Difference between revisions of "Glucocerebrosidase sequence based prediction"
From Bioinformatikpedia
(Created page with "== Secondary structure prediction == === General === === PSIPRED === === Jpred3 === === Comparison with DSSP === == Prediction of disordered regions == === General === ==…") |
(→PSIPRED) |
||
| Line 4: | Line 4: | ||
=== PSIPRED === |
=== PSIPRED === |
||
| + | |||
| + | PSIPRED is a method by David T. Jones, published 1999 in JMB with "Protein Secondary Structure Prediction Based on |
||
| + | Position-specific Scoring Matrices". PSIPRED works with a two-stage neural network to predict secondary structure. These are based on the position specifc scoring matrices generated by PSI-BLAST, which is run before. |
||
| + | |||
| + | We run the online and the local version of PSIPRED and got different results. In the following it is compared to the seconadry structere given in Uniprot<ref>http://www.uniprot.org/uniprot/P04062</ref>. |
||
| + | |||
| + | {| border="0" style="text-align:center; border-spacing:0;" |
||
| + | |Conf:||<code>988898954488887622315999999999998641038968865325999649995388</code> |
||
| + | |- |
||
| + | |online:||<code>CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCC</code> |
||
| + | |- |
||
| + | |Conf:||<code>987898955489988742200466888998986410038977877777863169974474</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>------------------------------------------------EEEE-EEEEEE-</code> |
||
| + | |- |
||
| + | |AA:||<code>MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNAT</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>558889998889992599996377885421237645688875108995378301079247</code> |
||
| + | |- |
||
| + | |online:||<code>CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEE</code> |
||
| + | |- |
||
| + | |Conf:||<code>148899998788875431100345640022100111177897107840966454557422</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEECCCCCCCEEEEE</code> |
||
| + | |- |
||
| + | |uniprot:||<code>-------------EEEEEEEE-----EEEEEEE-EEE----EEEEEEEEEEEEEE--EEE</code> |
||
| + | |- |
||
| + | |AA:||<code>YCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGF</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>300233899997249999999999860597882105999750588999986666899999</code> |
||
| + | |- |
||
| + | |online:||<code>EECCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC</code> |
||
| + | |- |
||
| + | |Conf:||<code>011335889987508927898998851396893001358621344677653324799999</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCHHHHHHHHHCCHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>EE--HHHHHHH----HHHHHHHHHHHH-CCCC---EEEEEEE--EEEEE------EEE--</code> |
||
| + | |- |
||
| + | |AA:||<code>GGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDD</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>689999994100245289999999971999389971377785612147247999889999</code> |
||
| + | |- |
||
| + | |online:||<code>CCCCCCCCCHHCCCCCHHHHHHHHHHCCCCCEEEECCCCCCCCCEECCCCCCCCCCCCCC</code> |
||
| + | |- |
||
| + | |Conf:||<code>721111368543220024799998733999689957899974220056347854325899</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>--------HHHH--HHHHHHHHHHH-----EEEEEEE---HHH----EEEEE-EEEE---</code> |
||
| + | |- |
||
| + | |AA:||<code>FQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQP</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>922699999999999999975490786872012579899999999986349999999999</code> |
||
| + | |- |
||
| + | |online:||<code>CCHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHH</code> |
||
| + | |- |
||
| + | |Conf:||<code>971468799999999967663395143898112789787678873222114422121122</code> |
||
| + | |- |
||
| + | |local:||<code>CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHH</code> |
||
| + | |- |
||
| + | |uniprot:||<code>-HHHHHHHHHHHHHHHHHHH-----EEEEE-----HHH------------HHHHHHHHHH</code> |
||
| + | |- |
||
| + | |AA:||<code>GDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIA</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>955799851689972999944888873334664149955640224689831699998033</code> |
||
| + | |- |
||
| + | |online:||<code>HHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHCCCHHHHCCCCEEEEEECCCCCCHHH</code> |
||
| + | |- |
||
| + | |Conf:||<code>111332310577410134212544556520222238976651151878702212236320</code> |
||
| + | |- |
||
| + | |local:||<code>HHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHCCCHHHHHCCEEEEEECCCCCCCCCC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>-HHHHHH--CCCCEEEEEEEEEHHH--HHHHHHH--HHHH----EEEEEEE------HHH</code> |
||
| + | |- |
||
| + | |AA:||<code>RDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAK</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>412688750999509994343699998866567831444255999999996402335772</code> |
||
| + | |- |
||
| + | |online:||<code>HHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEE</code> |
||
| + | |- |
||
| + | |Conf:||<code>011111126898001101210389653344579861210143212566552001100000</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHEEE</code> |
||
| + | |- |
||
| + | |uniprot:||<code>HHHHHHHH---EEEEEEEEE--------------HHHHHHHHHHHHHHHH--EEEEEEEE</code> |
||
| + | |- |
||
| + | |AA:||<code>ATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDW</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>000169999986689878535895679769986202333102244469939999542389</code> |
||
| + | |- |
||
| + | |online:||<code>EECCCCCCCCCCCCCCCCCCEEEECCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEECCC</code> |
||
| + | |- |
||
| + | |Conf:||<code>023699999860001325228998208703226821232123444679927984435078</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCCCCCCCCCEECCCCCCEEEEECCCCEEECCCEEEECCCCCCCCCCCEEEEEEEECC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>E-----------------EEEEEHHH-EEEE-HHHHHHHHHH-------EEEEEEEEE--</code> |
||
| + | |- |
||
| + | |AA:||<code>NLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQK</code> |
||
| + | |- |
||
| + | | |
||
| + | |- |
||
| + | |Conf:||<code>99028999928998999999099993779999099304998518951899999309</code> |
||
| + | |- |
||
| + | |online:||<code>CCCEEEEEECCCCCEEEEEECCCCCCEEEEEEECCCCEEEEECCCCEEEEEEEEEC</code> |
||
| + | |- |
||
| + | |Conf:||<code>99538995649997799999146898214741998642000389842568774139</code> |
||
| + | |- |
||
| + | |local:||<code>CCCCEEEEECCCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCCCCEEEEEEEECC</code> |
||
| + | |- |
||
| + | |uniprot:||<code>EEEEEEEE-----EEEEEEE-EEE-EEEEEEECCCEEEEEEE---EEEEEEE----</code> |
||
| + | |- |
||
| + | |AA:||<code>NDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ</code> |
||
| + | |} |
||
| + | |||
| + | The results differ a lot. The online version of PSIPRED seems to have different parameters than the local version. So we got different results. Compared to the given secondary structure in Uniprot there are many regions that are predicted wrong. |
||
=== Jpred3 === |
=== Jpred3 === |
||
Revision as of 10:03, 27 May 2011
Contents
Secondary structure prediction
General
PSIPRED
PSIPRED is a method by David T. Jones, published 1999 in JMB with "Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices". PSIPRED works with a two-stage neural network to predict secondary structure. These are based on the position specifc scoring matrices generated by PSI-BLAST, which is run before.
We run the online and the local version of PSIPRED and got different results. In the following it is compared to the seconadry structere given in Uniprot<ref>http://www.uniprot.org/uniprot/P04062</ref>.
| Conf: | 988898954488887622315999999999998641038968865325999649995388
|
| online: | CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCC
|
| Conf: | 987898955489988742200466888998986410038977877777863169974474
|
| local: | CCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC
|
| uniprot: | ------------------------------------------------EEEE-EEEEEE-
|
| AA: | MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNAT
|
| Conf: | 558889998889992599996377885421237645688875108995378301079247
|
| online: | CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEE
|
| Conf: | 148899998788875431100345640022100111177897107840966454557422
|
| local: | CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEECCCCCCCEEEEE
|
| uniprot: | -------------EEEEEEEE-----EEEEEEE-EEE----EEEEEEEEEEEEEE--EEE
|
| AA: | YCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGF
|
| Conf: | 300233899997249999999999860597882105999750588999986666899999
|
| online: | EECCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC
|
| Conf: | 011335889987508927898998851396893001358621344677653324799999
|
| local: | CCCCCHHHHHHHHHCCHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCC
|
| uniprot: | EE--HHHHHHH----HHHHHHHHHHHH-CCCC---EEEEEEE--EEEEE------EEE--
|
| AA: | GGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDD
|
| Conf: | 689999994100245289999999971999389971377785612147247999889999
|
| online: | CCCCCCCCCHHCCCCCHHHHHHHHHHCCCCCEEEECCCCCCCCCEECCCCCCCCCCCCCC
|
| Conf: | 721111368543220024799998733999689957899974220056347854325899
|
| local: | CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
|
| uniprot: | --------HHHH--HHHHHHHHHHH-----EEEEEEE---HHH----EEEEE-EEEE---
|
| AA: | FQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQP
|
| Conf: | 922699999999999999975490786872012579899999999986349999999999
|
| online: | CCHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
|
| Conf: | 971468799999999967663395143898112789787678873222114422121122
|
| local: | CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHH
|
| uniprot: | -HHHHHHHHHHHHHHHHHHH-----EEEEE-----HHH------------HHHHHHHHHH
|
| AA: | GDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIA
|
| Conf: | 955799851689972999944888873334664149955640224689831699998033
|
| online: | HHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHCCCHHHHCCCCEEEEEECCCCCCHHH
|
| Conf: | 111332310577410134212544556520222238976651151878702212236320
|
| local: | HHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHCCCHHHHHCCEEEEEECCCCCCCCCC
|
| uniprot: | -HHHHHH--CCCCEEEEEEEEEHHH--HHHHHHH--HHHH----EEEEEEE------HHH
|
| AA: | RDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAK
|
| Conf: | 412688750999509994343699998866567831444255999999996402335772
|
| online: | HHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEE
|
| Conf: | 011111126898001101210389653344579861210143212566552001100000
|
| local: | CCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHEEE
|
| uniprot: | HHHHHHHH---EEEEEEEEE--------------HHHHHHHHHHHHHHHH--EEEEEEEE
|
| AA: | ATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDW
|
| Conf: | 000169999986689878535895679769986202333102244469939999542389
|
| online: | EECCCCCCCCCCCCCCCCCCEEEECCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEECCC
|
| Conf: | 023699999860001325228998208703226821232123444679927984435078
|
| local: | CCCCCCCCCCCCEECCCCCCEEEEECCCCEEECCCEEEECCCCCCCCCCCEEEEEEEECC
|
| uniprot: | E-----------------EEEEEHHH-EEEE-HHHHHHHHHH-------EEEEEEEEE--
|
| AA: | NLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQK
|
| Conf: | 99028999928998999999099993779999099304998518951899999309
|
| online: | CCCEEEEEECCCCCEEEEEECCCCCCEEEEEEECCCCEEEEECCCCEEEEEEEEEC
|
| Conf: | 99538995649997799999146898214741998642000389842568774139
|
| local: | CCCCEEEEECCCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCCCCEEEEEEEECC
|
| uniprot: | EEEEEEEE-----EEEEEEE-EEE-EEEEEEECCCEEEEEEE---EEEEEEE----
|
| AA: | NDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ
|
The results differ a lot. The online version of PSIPRED seems to have different parameters than the local version. So we got different results. Compared to the given secondary structure in Uniprot there are many regions that are predicted wrong.
