Question: online software availability
0
gravatar for jananinithu
2.8 years ago by
jananinithu0 wrote:

Hi, I have a protein sequence and i need to mutate a sequence without changing the folds. Is there any tool available to check which amino acid residues in protein sequence can be mutated?

mutations tool • 832 views
ADD COMMENTlink modified 2.8 years ago by Michael Dondrup47k • written 2.8 years ago by jananinithu0

Please edit your question to contain enough detail to answer it. What do you mean by: "mutate a sequence without changing the folds". I guess you mean "which residues can be mutated without changing the structure of the protein (too much)"? What is your application of knowing these unconstrained residues?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Michael Dondrup47k

I think he wants to get a list of possible SNVs at a position from the given codon in the cDNA so he doesnt have to go through the ones that aren't biologically possible for an SNV.

ADD REPLYlink written 2.8 years ago by Ibrahim Tanyalcin1.1k

Like all synonymous codons? Certainly, that would keep the protein sequence identical.

.....Maybe.....

ADD REPLYlink written 2.8 years ago by Michael Dondrup47k

Btw.: If it's this I would use a chain of EMBOSS tools: transeq | backtranambig, that should output all ambiguous nucleotide sequences. However, if the application to express recombinant protein, it would be better to use backtranseq with a proper codon-frequency table.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Michael Dondrup47k
0
gravatar for Ibrahim Tanyalcin
2.8 years ago by
Belgium
Ibrahim Tanyalcin1.1k wrote:

Which protein are you interested in? I have couple graphs where you can check that, if I have the one you are looking for maybe I can help

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Ibrahim Tanyalcin1.1k

oph is the protein sequence

ADD REPLYlink written 2.8 years ago by jananinithu0

Sphingopyxis sp. (strain 113P3) with Uniprot ID of Q588Z2 ?

ADD REPLYlink written 2.8 years ago by Ibrahim Tanyalcin1.1k
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