[Edit : add clearer explanation] Hello,
So, I have cancer-normal RNA-seq and exome-seq data I downloaded from NCBI GEO (human). I have processed the data for getting gene expression level from the RNA-seq data set. Now, I want to do something else. What I want to do is so variant calling, either SNP or indel from the data set. I ahve done this before but now, I want to cross checking the mutation that occur in the genome to the protein sequence. I want to see if there are any changes in amino acid sequences derived from the gene that has mutation.
I want to ask for a tool that can help me to detect mutation (SNP, deletion, and/or insertion) and "translate" the aligned DNA sequence to amino acid sequence. From there, I want to check whether any change occur in the amino acid sequence by comparing to the protein sequence reference I get from PDB or Uniprot. I remember there is a blast tool that can compare nucleotide sequence to protein sequence but I want to include some mutation data. Thank you for your suggestion.