Hi,
Are there any tools to predict the effect of indel mutations on a protein? I have a dataset consisting of genomic coordinates of a large number of deletions that have been observed in patients and I need to infer the impact of these mutations on the amino acid sequence of a protein of interest (NRXN1). I.e. whether they cause a frameshift, complete loss of the protein or partial deletion of a portion of the amino acid sequence. Since there are tools to estimate the impact of single nucleotide variants, I am hoping that someone can point me in the direction of an equivalent tool for the (probably more challenging) problem of inferring the impact of genomic indels on an amino acid sequence. The specific example I am interested in has the added complexity of having two overlapping isoforms, encoding a shorter and a longer form of the amino acid sequence. If such tools exist, can I apply them separately on each coding sequence?
Cheers,
Sahar
VEP online tool: http://grch37.ensembl.org/Homo_sapiens/Tools/VEP
Or you can convert to VCF and run snpeff locally. VEP also runs locally, though it is not that trivial to install.
Thanks for your reply. Is this applicable for large indels? I dont have any information regarding the amino acid substitution change as the deletions are quite large.
Many thanks
Yes, it is.
As I don't have the genomic reference sequences for the set of indels that I have, is there any solution for this? I have a large number of indels to look at.
Many thanks.