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Are there any tools or R packages for calculating the new amino acid chain, given an indel?
I've been asked to provide a set of putative mutations, along with the novel peptides that result from these mutations. In the case of single amino acid and stop codon mutations, this is fairly easy, but for short indels that produce a frameshift (<10nt), this is non-trivial, for numerous reasons.
I'm currently trying to manually convert the coding sequences, based on the hgvs.c notation that I'm getting from snpEff, but while this seems to work for some, it doesn't seem to match well in other cases.
I would imagine that there is at least one tool for doing this, but all I can find are tools for calculating the hgsv codes, given a mutation, but no easy tool for calculating the resulting peptide.
Any help would be greatly appreciated!
I've been asked to provide a set of putative mutations, along with the novel peptides that result from these mutations. In the case of single amino acid and stop codon mutations, this is fairly easy, but for short indels that produce a frameshift (<10nt), this is non-trivial, for numerous reasons.
I'm currently trying to manually convert the coding sequences, based on the hgvs.c notation that I'm getting from snpEff, but while this seems to work for some, it doesn't seem to match well in other cases.
I would imagine that there is at least one tool for doing this, but all I can find are tools for calculating the hgsv codes, given a mutation, but no easy tool for calculating the resulting peptide.
Any help would be greatly appreciated!