Sequence-based mutation analysis HEXA

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Revision as of 14:40, 25 June 2011 by Link (talk | contribs) (Summary page)

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