Peptide generation from the identified mutations

Question

[Rucha.Wadapurkar]

I have identified SNPs using bioinformatics analysis and now I want to generate peptides for the identified SNPs. These SNPs are in huge number ~10000. How to do this? Are there any software/ tools available?

[iraun]

Hi! Welcome to Biostars :). Maybe you can take a look to these two links for some guidance and inspiration: How to get the mutated protein sequence from the DNA mutation information like the VCF or MAF file? and Generate peptide sequences from VCF . Personally, I have used Haplosaurus from VEP to reconstruct the mutated protein sequences, followed by a small custom script running sliding window of the desired peptide length.