Body: <p>Spoiler: This is probably a theoretical question. But, of course, if you have any tool that does this I will be extremely happy.</p>
  <p>So, I have WGS data for an organism O, both wild type (WT-O) and modified (M-O). I was able to assemble the reads using the O reference genome. Then, I was able to compare WT-O against M-O. I finally have the variants files (vcf), which I annotated with SnpEff and VEP.</p>
  <p>Now what I need to do is to evaluate the effect of the variants at protein level. What I know from the vcf files is which nucleotides were affected, their position, which chromosome, gene, and whatnot (in most cases, although this is not always true for all the variants).</p>
  <p>Question is: how to translate these variants from nucleotides to amino acids (AAs) and then, eventually, compare (BLAST?) the AAs sequences containing the variants to check whether they match with any known protein?</p>
  <p>EDIT:</p>
  <p>so the final goal would be to know whether the variants are causing some weird protein to be produced which may have a deleterious effect. It can be something like a toxin, or an allergen that are normally not present but that can appear &quot;by random chance&quot;. I need to make sure that nothing like that happened and to be sure i need to know which proteins may result from the variants.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-27T13:29:05.990Z
Comments.Text: Doesn't VEP provide the effect at the protein level? At the very least it should give the reference and modified amino acids, right? Can you please show us a few lines of your VCF so we know what you have to work with? Also, I assume you don't have a budget for paid tools here, right? The company I work for [has an API](https://api.varsome.com/) that can translate variants to HGVS protein notation and from that you can write a script that can build the protein sequence. But it's a paid service and you would still need to write your own script to get the full protein sequence.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-27T13:31:35.433Z
Comments.Text: Can you also give us some background on the biological question you are trying to answer? Why would you want to compare the proteins? It seem like a strange thing to do, I can't really think of why that would be useful. What is the final objective here? 
   What information do you want to get from this comparison? And what is this organism, does it have splicing or could you just translate the DNA directly?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T08:30:33.623Z
Comments.Text: @terdon, thank your for the link. i updated the question and i hope the final goal is more clear, now. also...i am not sure i can provide you with a sample from the VEP annotated file but i'll look into it.
Comments.UserDisplayName: gbt
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T08:33:12.300Z
Comments.Text: @terdon, maybe i have what i need in this VEP file, but it is not very clear to me how it works. i am quite new to this field of variant calling. i am looking into it.
Comments.UserDisplayName: gbt
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T14:21:37.257Z
Comments.Text: Just open the vcf file you have annotated with VEP, and show us a couple of variant lines with the annotations. Feel free to change the position/chromosome if you fear you cannot share it (although a couple of variants cannot be sensitive information). I want to see what kind of protein-level information you have. But the rest of your experiment doesn't really make sense to me. It sounds like you want to investigate the pathogenicity of the variants. There is no reason to try and re-create the protein and search for it, especially since the variants will often only change one amino acid.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-03T07:10:59.560Z
Comments.Text: @terdon, i understand but what if i need to have written proof of that? i need to make 100% sure that something unexpected happened.
Comments.UserDisplayName: gbt
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-03T13:22:56.403Z
Comments.Text: You don't need them all, you just need a structure on PDB then the question is solvable.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-04T08:34:14.627Z
Comments.Text: @M__ can you explain what you mean?
Comments.UserDisplayName: gbt
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-04T12:44:28.513Z
Comments.Text: You need a PDB file, without it I don't have a solution.
Comments.UserDisplayName: M__
Tags: <proteins><vcf><wgs><variants>
Title: how to annotate the effect of a genomic variant to predict what the resulting protein is?
ThreadText: # how to annotate the effect of a genomic variant to predict what the resulting protein is?
  
  (Asked by: username_0 on 2024-03-27)
  
  Spoiler: This is probably a theoretical question. But, of course, if you have any tool that does this I will be extremely happy.
  
  So, I have WGS data for an organism O, both wild type (WT-O) and modified (M-O). I was able to assemble the reads using the O reference genome. Then, I was able to compare WT-O against M-O. I finally have the variants files (vcf), which I annotated with SnpEff and VEP.
  
  Now what I need to do is to evaluate the effect of the variants at protein level. What I know from the vcf files is which nucleotides were affected, their position, which chromosome, gene, and whatnot (in most cases, although this is not always true for all the variants).
  
  Question is: how to translate these variants from nucleotides to amino acids (AAs) and then, eventually, compare (BLAST?) the AAs sequences containing the variants to check whether they match with any known protein?
  
  EDIT:
  
  so the final goal would be to know whether the variants are causing some weird protein to be produced which may have a deleterious effect. It can be something like a toxin, or an allergen that are normally not present but that can appear "by random chance". I need to make sure that nothing like that happened and to be sure i need to know which proteins may result from the variants.
  
  **Tags:** proteins, vcf, wgs, variants
  
  > **Comments:**
  > **username_1**: Doesn't VEP provide the effect at the protein level? At the very least it should give the reference and modified amino acids, right? Can you please show us a few lines of your VCF so we know what you have to work with? Also, I assume you don't have a budget for paid tools here, right? The company I work for [has an API](https://api.varsome.com/) that can translate variants to HGVS protein notation and from that you can write a script that can build the protein sequence. But it's a paid service and you would still need to write your own script to get the full protein sequence.  
  > **username_1**: Can you also give us some background on the biological question you are trying to answer? Why would you want to compare the proteins? It seem like a strange thing to do, I can't really think of why that would be useful. What is the final objective here?   What information do you want to get from this comparison? And what is this organism, does it have splicing or could you just translate the DNA directly?  
  > **username_0**: @username_1, thank your for the link. i updated the question and i hope the final goal is more clear, now. also...i am not sure i can provide you with a sample from the VEP annotated file but i'll look into it.  
  > **username_0**: @username_1, maybe i have what i need in this VEP file, but it is not very clear to me how it works. i am quite new to this field of variant calling. i am looking into it.  
  > **username_1**: Just open the vcf file you have annotated with VEP, and show us a couple of variant lines with the annotations. Feel free to change the position/chromosome if you fear you cannot share it (although a couple of variants cannot be sensitive information). I want to see what kind of protein-level information you have. But the rest of your experiment doesn't really make sense to me. It sounds like you want to investigate the pathogenicity of the variants. There is no reason to try and re-create the protein and search for it, especially since the variants will often only change one amino acid.  
  > **username_0**: @username_1, i understand but what if i need to have written proof of that? i need to make 100% sure that something unexpected happened.  
  > **username_2**: You don't need them all, you just need a structure on PDB then the question is solvable.  
  > **username_0**: @username_2 can you explain what you mean?  
  > **username_2**: You need a PDB file, without it I don't have a solution.  
  
  ---
  
  ## 0 answers
  
  