Difference between revisions of "Sequence-based mutation analysis HEXA"
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== Summary page == |
== Summary page == |
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| + | Here we sum up all analysis we did for the mutations: |
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| + | * pysicochemical properitites: we called a mutation neutral, if the properitites of the mutated amino acid are very similar to them of the orginal amino acid. Otherwise, it is called non-neutral. |
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| + | *visuale analysis: a mutation is called neutral, if the structure of the changed amino acid is very similar to the structure of the original amino acid. |
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| + | * PAM1, PAM2, BLOSUM62 and PSSM analysis: a mutation is called neutral, if the change score is near to the score of the most frequent exchanged amino acid. |
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| + | * multiple alignment: a mutation is called non-neutral if the original amino acid is very conserved in the alignment. If there is a conservation rate less than 50%, we decided to call the mutation neutral. |
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| + | * analysis with JPred, PsiPred: if the mutated amino acid has no secondary structure (coil) in the prediction of the secondary structure, we called the mutation neutral. |
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| + | * analysis with the real structure: here we look, if the mutation takes place in a secondary structure element or not. Instead of DSSP, we used the real structure. Normally, the real structure is not available and therefore, this value can not be used in the prediction. Therefore, we do not use this value, since we decided if the mutation is neutral or not. |
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| + | SNAP, SIFT and PolyPhen2 prediction: These are the three mutation prediction methods we used in our analysis. Here a mutation is called neutral, if the program predicts this mutation as neutral. |
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| + | In the table above you can see the summary of all of the analysis we did to got the possibility to make a statement about the mutation. Here we want to sum it up for each mutation and write it in the end down in an extra table. In the end, we wanted to compare our summing up with the reality and therefore we compared from which database the mutation was extracted. |
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| + | * Asn -> Ser |
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Revision as of 14:39, 25 June 2011
Mutations
| SNP-id | codon number | mutation codon | mutation triplet |
| rs4777505 | 29 | Asn -> Ser | AAC -> AGC |
| rs121907979 | 39 | Leu -> Arg | CTT -> CGT |
| rs61731240 | 179 | His -> Asp | CAT -> GAT |
| rs121907974 | 211 | Phe -> Ser | TTC -> TCC |
| rs61747114 | 248 | Leu -> Phe | CTT -> TTT |
| rs1054374 | 293 | Ser -> Ile | AGT -> ATT |
| rs121907967 | 329 | Trp -> TER | TGG -> TAG |
| rs1800430 | 399 | Asn -> Asp | AAC -> GAC |
| rs121907982 | 436 | Ile -> Val | ATA -> GTA |
| rs121907968 | 485 | Trp -> Arg | gTGG -> CGG |
Analysis of the mutations
We created for each mutation an extra page. The summary of the analysis can be seen in the Summary Section.
Summary page
Here we sum up all analysis we did for the mutations:
- pysicochemical properitites: we called a mutation neutral, if the properitites of the mutated amino acid are very similar to them of the orginal amino acid. Otherwise, it is called non-neutral.
- visuale analysis: a mutation is called neutral, if the structure of the changed amino acid is very similar to the structure of the original amino acid.
- PAM1, PAM2, BLOSUM62 and PSSM analysis: a mutation is called neutral, if the change score is near to the score of the most frequent exchanged amino acid.
- multiple alignment: a mutation is called non-neutral if the original amino acid is very conserved in the alignment. If there is a conservation rate less than 50%, we decided to call the mutation neutral.
- analysis with JPred, PsiPred: if the mutated amino acid has no secondary structure (coil) in the prediction of the secondary structure, we called the mutation neutral.
- analysis with the real structure: here we look, if the mutation takes place in a secondary structure element or not. Instead of DSSP, we used the real structure. Normally, the real structure is not available and therefore, this value can not be used in the prediction. Therefore, we do not use this value, since we decided if the mutation is neutral or not.
SNAP, SIFT and PolyPhen2 prediction: These are the three mutation prediction methods we used in our analysis. Here a mutation is called neutral, if the program predicts this mutation as neutral.
| method | mutations | |||||||||
| Asn -> Ser (rs4777505) | Leu -> Arg (rs121907979) | His -> Asp (rs61731240) | Phe -> Ser (rs121907974) | Leu -> Phe (rs61747114) | Ser -> Ile (rs1054374) | Trp -> TER (rs121907967) | Asn -> Asp (rs1800430) | Ile -> Val (rs121907982) | Trp -> Arg (rs121907968) | |
| pysiochemical properitites | neutral | non-neutral | non-neutral | non-neutral | neutral | non-neutral | non-neutral | neutral | neutral | non-neutral |
| visuale analysis | neutral | non-neutral | non-neutral | non-neutral | non-neutral | neutral | non-neutral | non-neutral | neutral | non-neutral |
| PAM1 | neutral | non-neutral | non-neutral | non-neutral | no statement | non-neutral | no information | neutral | neutral | neutral |
| PAM250 | neutral | non-neutral | no statement | non-neutral | no statement | no statement | no information | neutral | neutral | neutral |
| BLOSUM62 | neutral | no statement | no statement | non-neutral | neutral | non-neutral | no information | neutral | neutral | non-neutral |
| PSSM analysis | neutral | non-neutral | non-neutral | non-neutral | non-neutral | neutral | no information | neutral | neutral | non-neutral |
| multiple alignment | neutral | neutral | non-neutral | non-neutral | non-neutral | neutral | neutral | neutral | neutral | non-neutral |
| analysis with Jpred | non-neutral | non-neutral | neutral | neutral | neutral | neutral | neutral | neutral | neutral | neutral |
| analysis with PsiPred | non-neutral | non-neutral | neutral | neutral | neutral | neutral | neutral | non-neutral | neutral | neutral |
| analysis with real structure | non-neutral | no statement | neutral | neutral | non-neutral | neutral | non-neutral | no statement | non-neutral | non-neutral |
| SNAP Prediction | neutral | non-neutral | non-neutral | non-neutral | neutral | neutral | no information | neutral | neutral | non-neutral |
| SIFT Prediction | neutral | non-neutral | non-neutral | non-neutral | neutral | neutral | no information | neutral | neutral | non-neutral |
| PolyPhen2 Prediction | neutral | non-neutral | non-neutral | non-neutral | neutral | neutral | no information | neutral | neutral | non-neutral |
In the table above you can see the summary of all of the analysis we did to got the possibility to make a statement about the mutation. Here we want to sum it up for each mutation and write it in the end down in an extra table. In the end, we wanted to compare our summing up with the reality and therefore we compared from which database the mutation was extracted.
- Asn -> Ser
