How to ind out the difference in mutated and normal Protein

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    • #15835
      Steffi
      Participant

      Hello,

      I’m writing a project about malign tumours and their oncogenes. In my work I’m explaining some oncogenes, and these where mutations manifest themself in incorrect proteins, I want to study. I want to compare normal and mutated proteins via blast to see where the mutation is and what the consequences for e.g. signaling pathways are. So first I blasted normal Proteins like HGFR via blastp against the human proteome in ncbi to see which mutated sequences are available. My problem is that I didn’t found any sequences! Can anyone tell me a way to find mutated sequences of HGFR or CDK4 that lead to cancer? As an alternative, I searched for SNPs and fond some. But nowhere is annotated whether they are in intron/exon regions. Can anyone tell me how to find out?
      Please help a desperate student! 😀

    • #108694
      JackBean
      Participant

      here you will find the sequence of your protein. Then, if you have sequence of the mutated one, just align in by pairwise alignment

    • #108697
      Steffi
      Participant

      That’s just my problem. I have the sequence for my protein, but I couldn’t find any mutated sequences to compare…

    • #108698
      JackBean
      Participant

      Are they really mutated or just the expression is messed up?

    • #108699
      Steffi
      Participant

      They are really mutated.

    • #108722
      JackBean
      Participant

      and how do you know it?

    • #108723
      Steffi
      Participant

      While my studies for my procect, I found it out in an doctoral thesis. Do you have some ideas how to find the sequence of the mutated HGFR? Or how to find out if my founded SNPs are within an intron/exon region?

    • #108724
      JackBean
      Participant

      for searching the SNPs, just align the genomic version with cDNA and you will see the exon/intron boundaries.
      So they should have some sequence in the doctoral thesis, if they propose that it is mutated, right?

    • #108725
      Steffi
      Participant

      Not in this doctorial thesis, but I found one mutated nucleotide position in a citated paper. I hope I will find out which amino acid is affected by this. So I could see what’s wrong in the Protein HGFR.

    • #108726
      Steffi
      Participant

      But the alignment is a very good idea! It could have been my own idea… oO

    • #108737
      JackBean
      Participant
      quote Steffi:

      It could have been my own idea… oO

      it should

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