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How to ind out the difference in mutated and normal Protein

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How to ind out the difference in mutated and normal Protein

Postby Steffi » Mon Dec 12, 2011 9:28 pm

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! :D
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Re: How to ind out the difference in mutated and normal Protein

Postby JackBean » Tue Dec 13, 2011 11:25 am

here you will find the sequence of your protein. Then, if you have sequence of the mutated one, just align in by pairwise alignment
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby Steffi » Tue Dec 13, 2011 12:24 pm

That's just my problem. I have the sequence for my protein, but I couldn't find any mutated sequences to compare...
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Postby JackBean » Tue Dec 13, 2011 12:27 pm

Are they really mutated or just the expression is messed up?
http://www.biolib.cz/en/main/

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Postby Steffi » Tue Dec 13, 2011 12:57 pm

They are really mutated.
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Postby JackBean » Wed Dec 14, 2011 2:41 pm

and how do you know it?
http://www.biolib.cz/en/main/

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Postby Steffi » Wed Dec 14, 2011 3:13 pm

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?
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Postby JackBean » Wed Dec 14, 2011 4:51 pm

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?
http://www.biolib.cz/en/main/

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Postby Steffi » Wed Dec 14, 2011 7:51 pm

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.
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Postby Steffi » Wed Dec 14, 2011 7:54 pm

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

Postby JackBean » Thu Dec 15, 2011 1:07 pm

Steffi wrote:It could have been my own idea... oO

it should
http://www.biolib.cz/en/main/

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